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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):
print '\n Start common_part \n'
server_url = self.server_url
start_run = time.time()
refresh_num = 0
print '\n At 00 \n'
while True:
try:
print '\n At 01 \n'
final_body = self.getBody()
except:
time.sleep(5)
print '\n At 01-except \n'
final_body = self.getBody()
print '\n At 001 \n'
if final_body.find(auto_refresh_string) < 0:
break
time.sleep(13)
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'
print '\n At 02 \n'
if run_time > MAX_running_time :
self.fail('Run longer than MAX_running_time')
checkdoneUrl = server_url + self.getLastUrl()
print '\n checkdoneUrl = '
print checkdoneUrl
try:
print '\n At 03 \n'
gg = self.get(checkdoneUrl,
description="Get /cgi-bin/checkdone.cgi")
print '\n This is gg \n'
print str(gg)
except:
time.sleep(5)
print '\n At 03 - except \n'
gg = self.get(checkdoneUrl,
description="Get /cgi-bin/checkdone.cgi")
print '\n This is gg \n'
print str(gg)
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 Tnasas(FunkLoadTestCase):
"""XXX
This test use a configuration file Genesrf.conf.
"""
def setUp(self):
"""Setting up test."""
self.logd("setUp")
self.server_url = 'http://tnasas.bioinfo.cnio.es'
def test1(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("xdata2.txt")],
['class', Upload("Class")],
['model', 'dlda'],
['genesel', 'Fratio'],
['organism', 'None'],
['idtype', 'None']],
description="dlda and f ratio")
final_output = 'Classification algorithm: DLDA; gene selection using F statistic'
common_part(self, final_output)
def test2(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("xdata2.txt")],
['class', Upload("Class")],
['model', 'knn'],
['genesel', 'Wilcoxon'],
['organism', 'None'],
['idtype', 'None']],
description="knn and wilcoxon")
final_output = 'Classification algorithm: NN; gene selection using Wilcoxon statistic'
common_part(self, final_output)
def test3(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("xdata2.txt")],
['class', Upload("Class")],
['model', 'randomforest'],
['genesel', 'Fratio'],
['organism', 'None'],
['idtype', 'None']],
description="rF and Fratio")
final_output = 'Classification algorithm: Random forest; gene selection using F statistic'
common_part(self, final_output)
def test4(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("xdata2.txt")],
['class', Upload("Class")],
['model', 'svm'],
['genesel', 'randomforest'],
['organism', 'None'],
['idtype', 'None']],
description="svm and randomforest gene sel")
final_output = 'Classification algorithm: SVM (linear kernel); gene selection using Random Forest'
common_part(self, final_output)
def test5(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("xdata2.txt")],
['class', Upload("Class")],
['model', 'PAM'],
['genesel', 'Fratio'],
['organism', 'None'],
['idtype', 'None']],
description="PAM")
final_output = 'Classification algorithm: Shrunken centroids (PAM)'
common_part(self, final_output)
def test1_Named(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("./with.mm.names/short.covar2.txt")],
['class', Upload("./with.mm.names/class")],
['model', 'dlda'],
['genesel', 'Fratio'],
['organism', 'Mm'],
['idtype', 'ug']],
description="dlda and f ratio, Named")
final_output = 'Classification algorithm: DLDA; gene selection using F statistic'
common_part(self, final_output)
def test2_Named(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("./with.mm.names/short.covar2.txt")],
['class', Upload("./with.mm.names/class")],
['model', 'knn'],
['genesel', 'Wilcoxon'],
['organism', 'Mm'],
['idtype', 'ug']],
description="knn and wilcoxon, Named")
final_output = 'Classification algorithm: NN; gene selection using Wilcoxon statistic'
common_part(self, final_output)
def test3_Named(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("./with.mm.names/short.covar2.txt")],
['class', Upload("./with.mm.names/class")],
['model', 'randomforest'],
['genesel', 'Fratio'],
['organism', 'Mm'],
['idtype', 'ug']],
description="randomforest and f ratio, named")
final_output = 'Classification algorithm: Random forest; gene selection using F statistic'
common_part(self, final_output)
def test4_Named(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("./with.mm.names/short.covar2.txt")],
['class', Upload("./with.mm.names/class")],
['model', 'svm'],
['genesel', 'randomforest'],
['organism', 'Mm'],
['idtype', 'ug']],
description="svm and random forest, Named")
final_output = 'Classification algorithm: SVM (linear kernel); gene selection using Random Forest'
common_part(self, final_output)
def test5_Named(self):
server_url = self.server_url
self.get(server_url + "/",
description="Get /")
print '\n Start post \n'
self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[
['covariate', Upload("./with.mm.names/short.covar2.txt")],
['class', Upload("./with.mm.names/class")],
['model', 'PAM'],
['genesel', 'Fratio'],
['organism', 'Mm'],
['idtype', 'ug']],
description="PAM, Named")
final_output = 'Classification algorithm: Shrunken centroids (PAM)'
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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