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by ramon diaz-uriarte
initialized after cleaning up |
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# -*- coding: iso-8859-15 -*-
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"""basic_navigation FunkLoad test
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$Id: $
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"""
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import time |
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import unittest |
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from funkload.FunkLoadTestCase import FunkLoadTestCase |
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from webunit.utility import Upload |
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auto_refresh_string = 'This is an autorefreshing page' |
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MAX_running_time = 3600 * 1 |
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def common_part(self, final_output, |
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MAX_running_time = 3600, |
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auto_refresh_string = auto_refresh_string): |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start common_part \n' |
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1
by ramon diaz-uriarte
initialized after cleaning up |
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server_url = self.server_url |
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start_run = time.time() |
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refresh_num = 0 |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n At 00 \n' |
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by ramon diaz-uriarte
initialized after cleaning up |
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while True: |
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by ramon diaz-uriarte
(trying to) prevent false error reports |
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try: |
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print '\n At 01 \n' |
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final_body = self.getBody() |
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except: |
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time.sleep(5) |
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print '\n At 01-except \n' |
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final_body = self.getBody() |
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print '\n At 001 \n' |
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by ramon diaz-uriarte
initialized after cleaning up |
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if final_body.find(auto_refresh_string) < 0: |
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break
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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time.sleep(13) |
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1
by ramon diaz-uriarte
initialized after cleaning up |
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refresh_num += 1 |
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run_time = time.time() - start_run |
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print '\n Refreshed ' + str(refresh_num) + ' times. Been running for ' + str(round(run_time/60.0, 2)) + ' minutes.\n' |
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by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n At 02 \n' |
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by ramon diaz-uriarte
initialized after cleaning up |
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if run_time > MAX_running_time : |
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self.fail('Run longer than MAX_running_time') |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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checkdoneUrl = server_url + self.getLastUrl() |
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print '\n checkdoneUrl = ' |
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print checkdoneUrl |
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try: |
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print '\n At 03 \n' |
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gg = self.get(checkdoneUrl, |
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description="Get /cgi-bin/checkdone.cgi") |
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print '\n This is gg \n' |
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print str(gg) |
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except: |
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time.sleep(5) |
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print '\n At 03 - except \n' |
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gg = self.get(checkdoneUrl, |
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description="Get /cgi-bin/checkdone.cgi") |
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print '\n This is gg \n' |
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print str(gg) |
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27
by ramon diaz-uriarte
OKs when OK |
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expected = final_body.find(final_output) >= 0 |
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if not expected: |
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self.fail('\n ***** (begin of) Unexpected final result!!!! *****\n' + \ |
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by ramon diaz-uriarte
better error messages |
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str(final_body) + \ |
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'\n ***** (end of) Unexpected final result!!!! *****\n') |
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by ramon diaz-uriarte
OKs when OK |
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else: |
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print 'OK' |
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1
by ramon diaz-uriarte
initialized after cleaning up |
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class Tnasas(FunkLoadTestCase): |
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"""XXX
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This test use a configuration file Genesrf.conf.
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"""
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def setUp(self): |
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"""Setting up test."""
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self.logd("setUp") |
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self.server_url = 'http://tnasas.bioinfo.cnio.es' |
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def test1(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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by ramon diaz-uriarte
initialized after cleaning up |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("xdata2.txt")], |
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['class', Upload("Class")], |
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['model', 'dlda'], |
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['genesel', 'Fratio'], |
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['organism', 'None'], |
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['idtype', 'None']], |
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description="dlda and f ratio") |
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final_output = 'Classification algorithm: DLDA; gene selection using F statistic' |
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common_part(self, final_output) |
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def test2(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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by ramon diaz-uriarte
initialized after cleaning up |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("xdata2.txt")], |
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['class', Upload("Class")], |
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['model', 'knn'], |
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['genesel', 'Wilcoxon'], |
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['organism', 'None'], |
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['idtype', 'None']], |
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description="knn and wilcoxon") |
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final_output = 'Classification algorithm: NN; gene selection using Wilcoxon statistic' |
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common_part(self, final_output) |
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def test3(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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1
by ramon diaz-uriarte
initialized after cleaning up |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("xdata2.txt")], |
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['class', Upload("Class")], |
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['model', 'randomforest'], |
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['genesel', 'Fratio'], |
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['organism', 'None'], |
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['idtype', 'None']], |
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34
by RDU
Tnasas: genes with UG name |
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description="rF and Fratio") |
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1
by ramon diaz-uriarte
initialized after cleaning up |
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final_output = 'Classification algorithm: Random forest; gene selection using F statistic' |
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common_part(self, final_output) |
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def test4(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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1
by ramon diaz-uriarte
initialized after cleaning up |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("xdata2.txt")], |
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['class', Upload("Class")], |
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['model', 'svm'], |
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['genesel', 'randomforest'], |
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['organism', 'None'], |
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['idtype', 'None']], |
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34
by RDU
Tnasas: genes with UG name |
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description="svm and randomforest gene sel") |
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1
by ramon diaz-uriarte
initialized after cleaning up |
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final_output = 'Classification algorithm: SVM (linear kernel); gene selection using Random Forest' |
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common_part(self, final_output) |
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def test5(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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by ramon diaz-uriarte
initialized after cleaning up |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("xdata2.txt")], |
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['class', Upload("Class")], |
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['model', 'PAM'], |
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['genesel', 'Fratio'], |
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['organism', 'None'], |
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['idtype', 'None']], |
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34
by RDU
Tnasas: genes with UG name |
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description="PAM") |
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final_output = 'Classification algorithm: Shrunken centroids (PAM)' |
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common_part(self, final_output) |
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def test1_Named(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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34
by RDU
Tnasas: genes with UG name |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("./with.mm.names/short.covar2.txt")], |
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['class', Upload("./with.mm.names/class")], |
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['model', 'dlda'], |
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['genesel', 'Fratio'], |
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['organism', 'Mm'], |
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['idtype', 'ug']], |
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description="dlda and f ratio, Named") |
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final_output = 'Classification algorithm: DLDA; gene selection using F statistic' |
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common_part(self, final_output) |
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def test2_Named(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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34
by RDU
Tnasas: genes with UG name |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("./with.mm.names/short.covar2.txt")], |
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['class', Upload("./with.mm.names/class")], |
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['model', 'knn'], |
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['genesel', 'Wilcoxon'], |
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['organism', 'Mm'], |
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['idtype', 'ug']], |
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description="knn and wilcoxon, Named") |
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final_output = 'Classification algorithm: NN; gene selection using Wilcoxon statistic' |
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common_part(self, final_output) |
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def test3_Named(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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34
by RDU
Tnasas: genes with UG name |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("./with.mm.names/short.covar2.txt")], |
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['class', Upload("./with.mm.names/class")], |
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['model', 'randomforest'], |
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['genesel', 'Fratio'], |
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['organism', 'Mm'], |
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['idtype', 'ug']], |
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description="randomforest and f ratio, named") |
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final_output = 'Classification algorithm: Random forest; gene selection using F statistic' |
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common_part(self, final_output) |
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def test4_Named(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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34
by RDU
Tnasas: genes with UG name |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("./with.mm.names/short.covar2.txt")], |
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['class', Upload("./with.mm.names/class")], |
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['model', 'svm'], |
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['genesel', 'randomforest'], |
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['organism', 'Mm'], |
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['idtype', 'ug']], |
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description="svm and random forest, Named") |
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final_output = 'Classification algorithm: SVM (linear kernel); gene selection using Random Forest' |
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common_part(self, final_output) |
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def test5_Named(self): |
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server_url = self.server_url |
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self.get(server_url + "/", |
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description="Get /") |
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78
by ramon diaz-uriarte
(trying to) prevent false error reports |
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print '\n Start post \n' |
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34
by RDU
Tnasas: genes with UG name |
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self.post(server_url + "/cgi-bin/tnasasR.cgi", params=[ |
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['covariate', Upload("./with.mm.names/short.covar2.txt")], |
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['class', Upload("./with.mm.names/class")], |
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['model', 'PAM'], |
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['genesel', 'Fratio'], |
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['organism', 'Mm'], |
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['idtype', 'ug']], |
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description="PAM, Named") |
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final_output = 'Classification algorithm: Shrunken centroids (PAM)' |
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common_part(self, final_output) |
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1
by ramon diaz-uriarte
initialized after cleaning up |
244 |
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def tearDown(self): |
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"""Setting up test."""
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self.logd("tearDown.\n") |
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if __name__ in ('main', '__main__'): |
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unittest.main() |