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# -*- coding: iso-8859-15 -*-
"""basic_navigation FunkLoad test
$Id: $
"""
import time
import unittest
from funkload.FunkLoadTestCase import FunkLoadTestCase
from webunit.utility import Upload
auto_refresh_string = 'This is an autorefreshing page'
MAX_running_time = 3600 * 1
def common_part(self, final_output,
MAX_running_time = 3600,
auto_refresh_string = auto_refresh_string):
server_url = self.server_url
start_run = time.time()
refresh_num = 0
while True:
final_body = self.getBody()
if final_body.find(auto_refresh_string) < 0:
break
time.sleep(32)
refresh_num += 1
run_time = time.time() - start_run
print '\n Refreshed ' + str(refresh_num) + ' times. Been running for ' + str(round(run_time/60.0, 2)) + ' minutes.\n'
if run_time > MAX_running_time :
self.fail('Run longer than MAX_running_time')
self.get(server_url + self.getLastUrl(),
description="Get /cgi-bin/checkdone.cgi")
expected = final_body.find(final_output) >= 0
if not expected:
self.fail('\n ***** (begin of) Unexpected final result!!!! *****\n' + \
str(final_body) + \
'\n ***** (end of) Unexpected final result!!!! *****\n')
else:
print 'OK'
class Signs(FunkLoadTestCase):
"""XXX
This test use a configuration file Signs.conf.
"""
def setUp(self):
"""Setting up test."""
self.logd("setUp")
self.server_url = 'http://signs.bioinfo.cnio.es'
##self.server_url = self.conf_get('main', 'url')
def test1(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
self.post(server_url + "/cgi-bin/signsR.cgi", params=[
['covariate', Upload("./test1/mini.lung.covar.txt")],
['time', Upload("./test1/mini.lung.surv.txt")],
['event', Upload("./test1/mini.lung.event.txt")],
## ['validation', 'on'],
['validationcovariate', Upload("./test1/empty.txt")],
['validationtime', Upload("./test1/empty.txt")],
['validationevent', Upload("./test1/empty.txt")],
['methodSurv', 'FCMS'],
['Minp', '0.1'],
['MaxSize', '100'],
['MinSize', '10'],
['MinCor', '0.5'],
['organism', 'None'],
['idtype', 'None']],
description="Post /cgi-bin/signsR.cgi")
final_output = 'No groups that meet the p, minimum correlation and size restrictions.'
common_part(self, final_output)
def test2(self):
# The description should be set in the configuration file
server_url = self.server_url
# begin of test ---------------------------------------------
self.get(server_url + "/",
description="Get /")
self.post(server_url + "/cgi-bin/signsR.cgi", params=[
['covariate', Upload("./test2/mini.lung.covar.txt")],
['time', Upload("./test2/mini.lung.surv.txt")],
['event', Upload("./test2/mini.lung.event.txt")],
['validation', 'on'],
['validationcovariate', Upload("./test2/empty.txt")],
['validationtime', Upload("./test2/empty.txt")],
['validationevent', Upload("./test2/empty.txt")],
['methodSurv', 'FCMS'],
['Minp', '0.1'],
['MaxSize', '100'],
['MinSize', '10'],
['MinCor', '0.5'],
['organism', 'None'],
['idtype', 'None']],
description="Post /cgi-bin/signsR.cgi")
final_output = '<h1> SignS INPUT ERROR </h1>\n<p> validationcovariate file has size 0 </p>'
common_part(self, final_output, MAX_running_time = 30)
def test_division_by_zero(self):
# The description should be set in the configuration file
server_url = self.server_url
# begin of test ---------------------------------------------
self.get(server_url + "/",
description="Get /")
self.post(server_url + "/cgi-bin/signsR.cgi", params=[
['covariate', Upload("./division.by.zero/covariate")],
['time', Upload("./division.by.zero/time")],
['event', Upload("./division.by.zero/event")],
# ['validation', 'on'],
# ['validationcovariate', Upload("./test2/empty.txt")],
# ['validationtime', Upload("./test2/empty.txt")],
# ['validationevent', Upload("./test2/empty.txt")],
['methodSurv', 'FCMS'],
['Minp', '0.5'],
['MaxSize', '100'],
['MinSize', '2'],
['MinCor', '0.2'],
['organism', 'None'],
['idtype', 'None']],
description="Division by zero")
MAX_running_time = 3600 * 6
final_output = '<p> Total of 2 signature components selected and 72 genes.</p>'
common_part(self, final_output)
# def test3(self):
# # The description should be set in the configuration file
# server_url = self.server_url
# # begin of test ---------------------------------------------
# self.get(server_url + "/",
# description="Get /")
# self.post(server_url + "/cgi-bin/signsR.cgi", params=[
# ['covariate', Upload("./test3/covar")],
# ['time', Upload("./test3/time")],
# ['event', Upload("./test3/event")],
# # ['validation', 'on'],
# # ['validationcovariate', Upload("./test2/empty.txt")],
# # ['validationtime', Upload("./test2/empty.txt")],
# # ['validationevent', Upload("./test2/empty.txt")],
# ['methodSurv', 'FCMS'],
# ['Minp', '0.5'],
# ['MaxSize', '100'],
# ['MinSize', '2'],
# ['MinCor', '0.2'],
# ['organism', 'None'],
# ['idtype', 'None']],
# description="Division by zero")
# final_output = '<p> Total of 2 signature components selected and 72 genes.</p>'
# common_part(self, final_output)
def test3_validation(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
self.post(server_url + "/cgi-bin/signsR.cgi", params=[
['covariate', Upload("./test3/covar")],
['time', Upload("./test3/time")],
['event', Upload("./test3/event")],
['validation', 'on'],
['validationcovariate', Upload("./test3/covar")],
['validationtime', Upload("./test3/time")],
['validationevent', Upload("./test3/event")],
['methodSurv', 'FCMS'],
['Minp', '0.7'],
['MaxSize', '100'],
['MinSize', '2'],
['MinCor', '0.4'],
['organism', 'None'],
['idtype', 'None']],
description="Division by zero")
final_output = '<p> Total of 2 signature components selected and 63 genes.</p>'
common_part(self, final_output)
def test_apache2(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
self.post(server_url + "/cgi-bin/signsR.cgi", params=[
['covariate', Upload("./apache-prob2/covariate")],
['time', Upload("./apache-prob2/class_labels")],
['event', Upload("./apache-prob2/survival_time")],
['methodSurv', 'FCMS'],
['Minp', '0.7'],
['MaxSize', '100'],
['MinSize', '2'],
['MinCor', '0.4'],
['organism', 'None'],
['idtype', 'None']],
description="More than one Name line")
final_output = 'You have more than one line with #Name (or #NAME or #name), in the data matrix '
common_part(self, final_output)
def test_apache3(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
self.post(server_url + "/cgi-bin/signsR.cgi", params=[
['covariate', Upload("./apache-prob3/covariate")],
['time', Upload("./apache-prob3/class_labels")],
['event', Upload("./apache-prob3/survival_time")],
['methodSurv', 'FCMS'],
['Minp', '0.05'],
['MaxSize', '100'],
['MinSize', '5'],
['MinCor', '0.8'],
['organism', 'None'],
['idtype', 'None']],
description=' Name with "')
final_output = 'Total of 1 signature components selected and 8 genes'
common_part(self, final_output)
def test_signs_pals(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
self.post(server_url + "/cgi-bin/signsR.cgi", params=[
['covariate', Upload("./names-genes/covariate")],
['time', Upload("./names-genes/time")],
['event', Upload("./names-genes/event")],
['methodSurv', 'FCMS'],
['Minp', '0.1'],
['MaxSize', '100'],
['MinSize', '10'],
['MinCor', '0.5'],
['organism', 'Mm'],
['idtype', 'ug']],
description=' Test PaLS-valid output')
final_output = 'Total of 2 signature components selected and 26 genes.'
common_part(self, final_output)
def test_signs_pals_should_not_crash(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
self.post(server_url + "/cgi-bin/signsR.cgi", params=[
['covariate', Upload("./names-genes/covariate")],
['time', Upload("./names-genes/event")],
['event', Upload("./names-genes/time")],
['methodSurv', 'FCMS'],
['Minp', '0.1'],
['MaxSize', '100'],
['MinSize', '10'],
['MinCor', '0.5'],
['organism', 'Mm'],
['idtype', 'ug']],
description=' Used to cause an "Surv(time, event) : Invalid status value"')
final_output = 'Your status data is not valid; can only be 0 or 1'
common_part(self, final_output)
def tearDown(self):
"""Setting up test."""
self.logd("tearDown.\n")
if __name__ in ('main', '__main__'):
unittest.main()
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