"""
Web server testing code for PDB2PQR
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calculations
Copyright (c) 2002-2010, Jens Erik Nielsen, University College Dublin;
Nathan A. Baker, Washington University in St. Louis; Paul Czodrowski &
Gerhard Klebe, University of Marburg
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the names of University College Dublin, Washington University in
St. Louis, or University of Marburg nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
OF THE POSSIBILITY OF SUCH DAMAGE.
----------------------------
"""
__date__ = "26 January 2010"
__author__ = "Samir Unni, Yong Huang"
import urllib, urllib2, time, StringIO
import os
import random
from sys import argv
rand = int(random.random()*3) + 1 # Creating a random integer in {1,2,3}
def launchJob(pdbID):
url = 'http://pdb2pqr-%s/pdb2pqr/pdb2pqr.cgi' % (rand)
values = {'TEXTCONTROL' : 'ID',
'PDBID' : pdbID,
'FF' : 'amber',
'FFOUT' : 'internal',
'DEBUMP' : 'CHECKED',
'OPT' : 'CHECKED'}
data = urllib.urlencode(values)
req = urllib2.Request(url, data)
response = urllib2.urlopen(req)
for i in range(0,2):
response.readline()
url = response.readline()[45:-3]
return url
def checkJob(url):
response = open(urllib.urlretrieve(url)[0])
while True:
status = response.readline()
if status[0:7]=="Message":
status = status[9:-7].strip()
break
elif status=='':
break
return status
def main():
#---User configurable values---
threads = 100 # number of simultaneous calculations
timeout = 1000 # timeout in seconds (before a job is considered failed)
sleeptime = 30 # how long to wait between checks in seconds
#------------------------
currentdir = os.getcwd()
webtestdir = currentdir + '/tests/test-webserver/'
listFile = open(webtestdir+'lst','r')
pdbIDs = listFile.read().strip().split('\n')
listFile.close()
currentID = 0
currentJobs = []
completedJobs = []
failedJobs = []
timeout = timeout/sleeptime
while(currentID<len(pdbIDs) or len(currentJobs)>0):
while(len(currentJobs)<threads and currentID<len(pdbIDs)):
pdbID = pdbIDs[currentID].strip()
print "launching %s" % pdbID
currentJobs.append([pdbID,launchJob(pdbID),0])
print "%i threads" % threads
currentID = currentID+1
print "sleeping"
time.sleep(sleeptime)
jobsToDelete = []
for i in range(0,len(currentJobs)):
print currentJobs[i]
print "checking %s" % currentJobs[i][0]
result = checkJob(currentJobs[i][1])
print "%s: %s" % (currentJobs[i][0], result)
if(result=="complete" or result=="failed"):
completedJobs.append([currentJobs[i][0], result])
jobsToDelete.append(i)
elif currentJobs[i][2]>timeout:
print "%s: failed" % currentJobs[i][0]
completedJobs.append([currentJobs[i][0], "failed"])
jobsToDelete.append(i)
else:
currentJobs[i][2] = currentJobs[i][2]+1
print "jobsToDelete: %s" % jobsToDelete
jobsToDelete.reverse()
for i in jobsToDelete:
print "i = %i" % i
print "deleting %s" % currentJobs[i][0]
del currentJobs[i]
for i in range(0,len(completedJobs)):
if(completedJobs[i][1]=="failed"):
failedJobs.append(completedJobs[i][0])
if len(failedJobs) == 0:
print "\nWeb test finished with no failed jobs.\n"
else:
print "\nThese jobs failed: %s.\n" % (failedJobs)
if __name__ == "__main__":
main()
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