def redirector(name, weboptions):
"""
Prints a page which redirects the user to querystatus.cgi and writes starting time to file
"""
redirectWait = 3
utilities.startLogFile(name, 'pdb2pqr_start_time', str(time.time()))
jobid = int(name)
analiticsDict = weboptions.getOptions()
events = {}
events['submission'] = analiticsDict['pdb']+'|'+str(os.environ["REMOTE_ADDR"])
del analiticsDict['pdb']
events['titration'] = str(analiticsDict.get('ph'))
if 'ph' in analiticsDict:
del analiticsDict['ph']
events['apbsInput'] = str(analiticsDict.get('apbs'))
del analiticsDict['apbs']
#Clean up selected extensions output
if 'selectedExtensions' in analiticsDict:
analiticsDict['selectedExtensions'] = ' '.join(analiticsDict['selectedExtensions'])
options = ','.join(str(k)+':'+str(v) for k,v in analiticsDict.items())
events['options']=options
eventsScriptString = ''
for event in events:
eventsScriptString += utilities.getEventTrackingString(category='submissionData',
action=event,
label=events[event])
redirectURL = "{website}querystatus.cgi?jobid={jobid}&calctype=pdb2pqr".format(website=WEBSITE,
jobid=jobid)
string = """
<html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<meta http-equiv="Refresh" content="{wait}; url={redirectURL}">
<link rel="stylesheet" href="{website}pdb2pqr.css"type="text/css">
</head>
<body>
<center>
You are being automatically redirected to a new location.<br />
If your browser does not redirect you in {wait} seconds, or you do
not wish to wait, <a href="{redirectURL}">click here</a></center>.
</body>
</html>""".format(trackingscript=utilities.getTrackingScriptString(jobid=jobid),
trackingevents=eventsScriptString, redirectURL=redirectURL, wait=redirectWait, website=WEBSITE)
return string
def main(apbsOptions):
cgiFile = "jmol.cgi"
cgiName = "thisform"
defaultVisType = "jmol"
checkJmolType = True
cssFile = 'pdb2pqr.css'
jobid = form['jobid'].value
string = """
<html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<title>Visualization</title>
<link rel="stylesheet" href="pdb2pqr.css" type="text/css">
<script type="text/JavaScript" src="jmol/Jmol.js"></script>
<script type="text/JavaScript">APPLET_PATH="jmol/";GZIP=""</script>
<script type="text/JavaScript" src="jmol/apbsjmol.js"></script>
</head>
<body onload="init()">
<script type="text/javascript">createVisualization({jobid}, -5.0, 5.0)</script>
</body>
</html>""".format(jobid=jobid,
trackingevents=getEventTrackingString(category='apbs',
action='visualize',
label=str(os.environ["REMOTE_ADDR"])),
trackingscript=getTrackingScriptString(jobid=jobid))
print string
def main(apbsOptions):
cgiFile = "jmol.cgi"
cgiName = "thisform"
defaultVisType = "jmol"
checkJmolType = True
cssFile = 'pdb2pqr.css'
jobid = form['jobid'].value
string = """
<html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<title>Visualization</title>
<link rel="stylesheet" href="pdb2pqr.css" type="text/css">
<script type="text/JavaScript" src="jmol/Jmol.js"></script>
<script type="text/JavaScript">APPLET_PATH="jmol/";GZIP=""</script>
<script type="text/JavaScript" src="jmol/apbsjmol.js"></script>
</head>
<body onload="init()">
<script type="text/javascript">createVisualization({jobid}, -5.0, 5.0)</script>
</body>
</html>""".format(jobid=jobid,
trackingevents=getEventTrackingString(
category='apbs',
action='visualize',
label=str(os.environ["REMOTE_ADDR"])),
trackingscript=getTrackingScriptString(jobid=jobid))
print string
def redirector(name, weboptions):
"""
Prints a page which redirects the user to querystatus.cgi and writes starting time to file
"""
redirectWait = 3
utilities.startLogFile(name, 'pdb2pqr_start_time', str(time.time()))
jobid = int(name)
analiticsDict = weboptions.getOptions()
events = {}
events['submission'] = analiticsDict['pdb']+'|'+str(os.environ["REMOTE_ADDR"])
del analiticsDict['pdb']
events['titration'] = str(analiticsDict.get('ph'))
if 'ph' in analiticsDict:
del analiticsDict['ph']
events['apbsInput'] = str(analiticsDict.get('apbs'))
del analiticsDict['apbs']
#Clean up selected extensions output
if 'selectedExtensions' in analiticsDict:
analiticsDict['selectedExtensions'] = ' '.join(analiticsDict['selectedExtensions'])
options = ','.join(str(k)+':'+str(v) for k,v in analiticsDict.items())
events['options']=options
eventsScriptString = ''
for event in events:
eventsScriptString += utilities.getEventTrackingString(category='submissionData',
action=event,
label=events[event])
redirectURL = "{website}querystatus.cgi?jobid={jobid}&calctype=pdb2pqr".format(website=WEBSITE,
jobid=jobid)
string = """
<html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<meta http-equiv="Refresh" content="{wait}; url={redirectURL}">
<link rel="stylesheet" href="{website}pdb2pqr.css"type="text/css">
</head>
<body>
<center>
You are being automatically redirected to a new location.<br />
If your browser does not redirect you in {wait} seconds, or you do
not wish to wait, <a href="{redirectURL}">click here</a></center>.
</body>
</html>""".format(trackingscript=utilities.getTrackingScriptString(jobid=jobid),
trackingevents=eventsScriptString, redirectURL=redirectURL, wait=redirectWait, website=WEBSITE)
return string
def main(apbsOptions):
cgiFile = "jmol.cgi"
cgiName = "thisform"
defaultVisType = "jmol"
checkJmolType = True
cssFile = 'pdb2pqr.css'
jobid = form['jobid'].value
string = """
<!DOCTYPE html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<title>Visualization</title>
<link rel="stylesheet" href="3dmol/css/pdb2pqr_3dmol.css" type="text/css">
<link rel="stylesheet" href="3dmol/css/foundation.css">
<link rel="stylesheet" type="text/css" href="3dmol/css/pure-min.css" media="screen" />
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
<script src="http://3dmol.csb.pitt.edu/build/3Dmol.js"></script>
<script type="text/JavaScript" src="3dmol/js/visualize_html.js"></script>
<script type="text/JavaScript" src="3dmol/js/3dmol.js"></script>
</head>
<body>
<script type="text/javascript">build_page({jobid})</script>
<script type="text/javascript">getpqr({jobid})</script>
</body>
</html>""".format(jobid=jobid,
trackingevents=getEventTrackingString(
category='apbs',
action='visualize',
label=str(os.environ["REMOTE_ADDR"])),
trackingscript=getTrackingScriptString(jobid=jobid))
print string
def main(apbsOptions):
cgiFile = "jmol.cgi"
cgiName = "thisform"
defaultVisType = "jmol"
checkJmolType = True
cssFile = 'pdb2pqr.css'
jobid = form['jobid'].value
string = """
<!DOCTYPE html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<title>Visualization</title>
<link rel="stylesheet" href="3dmol/css/pdb2pqr_3dmol.css" type="text/css">
<link rel="stylesheet" href="3dmol/css/foundation.css">
<link rel="stylesheet" type="text/css" href="3dmol/css/pure-min.css" media="screen" />
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
<script src="http://3dmol.csb.pitt.edu/build/3Dmol.js"></script>
<script type="text/JavaScript" src="3dmol/js/visualize_html.js"></script>
<script type="text/JavaScript" src="3dmol/js/3dmol.js"></script>
</head>
<body>
<script type="text/javascript">build_page({jobid})</script>
<script type="text/javascript">getpqr({jobid})</script>
</body>
</html>""".format(jobid=jobid,
trackingevents=getEventTrackingString(category='apbs',
action='visualize',
label=str(os.environ["REMOTE_ADDR"])),
trackingscript=getTrackingScriptString(jobid=jobid))
print string
def mainCGI():
"""
Main method for determining the query page output
"""
logopts = {}
print "Content-type: text/html\n\n"
calctype = form["calctype"].value
# prints version error, if it exists
if form["jobid"].value == 'False':
print printheader("%s Job Status Page" % calctype.upper())
progress = "version_mismatch"
runtime = 0
elif form["jobid"].value == 'notenoughmem':
print printheader("%s Job Status Page" % calctype.upper())
progress = "not_enough_memory"
runtime = 0
else:
progress = None
#Check for error html
errorpath = '%s%s%s.html' % (INSTALLDIR, TMPDIR, form["jobid"].value)
if os.path.isfile(errorpath):
string = ""
string += "<html>\n"
string += "\t<head>\n"
string += "\t\t<meta http-equiv=\"Refresh\" content=\"0; url=%s%s%s.html\">\n" % (
WEBSITE, TMPDIR, form["jobid"].value)
string += "\t</head>\n"
string += "</html>\n"
print string
return
# prepares for Opal query, if necessary
if have_opal:
if calctype == "pdb2pqr":
opal_url = PDB2PQR_OPAL_URL
elif calctype == "apbs":
opal_url = APBS_OPAL_URL
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(opal_url)
else:
appServicePort = None
# if PDB2PQR, determines if link to APBS calculation should be shown
if calctype == "pdb2pqr":
#if(form["apbsinput"].value=="True"): # change to use a file
# apbs_input = True
#else:
# apbs_input = False
apbsInputFile = open('%s%s%s/apbs_input' %
(INSTALLDIR, TMPDIR, form["jobid"].value))
apbs_input = apbsInputFile.read()
apbsInputFile.close()
if apbs_input == "True":
apbs_input = True
else:
apbs_input = False
typemapInputFile = open('%s%s%s/typemap' %
(INSTALLDIR, TMPDIR, form["jobid"].value))
typemap = typemapInputFile.read()
typemapInputFile.close()
if typemap == "True":
typemap = True
else:
typemap = False
if have_opal and progress == None:
if form["calctype"].value == "pdb2pqr":
pdb2pqrJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' %
(INSTALLDIR, TMPDIR, form["jobid"].value))
jobid = pdb2pqrJobIDFile.read()
pdb2pqrJobIDFile.close()
elif form["calctype"].value == "apbs":
apbsJobIDFile = open('%s%s%s/apbs_opal_job_id' %
(INSTALLDIR, TMPDIR, form["jobid"].value))
jobid = apbsJobIDFile.read()
apbsJobIDFile.close()
else:
jobid = form["jobid"].value
if progress == None:
cp = checkprogress(jobid, appServicePort,
calctype) # finds out status of job
progress = cp[0]
#initialize with bogus value just in case
starttime = time.time()
if progress == "running" or progress == "complete":
timefile = open(
'%s%s%s/%s_start_time' %
(INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value))
starttime = float(timefile.read())
timefile.close()
if progress == "running" or (have_opal and progress not in (
"version_mismatch", "not_enough_memory", "error", "complete")):
runtime = time.time() - starttime
elif progress == "complete":
endTimeFileString = '%s%s%s/%s_end_time' % (
INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value)
if have_opal and not os.path.isfile(endTimeFileString):
runtime = time.time() - starttime
with open(endTimeFileString, 'w') as endTimeFile:
endTimeFile.write(str(time.time()))
else:
with open(endTimeFileString, 'r') as endTimeFile:
runtime = float(endTimeFile.read()) - starttime
else:
runtime = -1
if progress == "running":
#if have_opal:
# resultsurl = cp[1]._baseURL
#else:
if calctype == "pdb2pqr":
resultsurl = '%squerystatus.cgi?jobid=%s&apbsinput=%s&calctype=pdb2pqr' % (
WEBSITE, form["jobid"].value, apbs_input)
else:
resultsurl = '%squerystatus.cgi?jobid=%s&calctype=apbs' % (
WEBSITE, form["jobid"].value)
if progress == "complete":
print printheader("%s Job Status Page" % calctype.upper(),
jobid=form["jobid"].value)
elif progress == "error":
print printheader("%s Job Status Page - Error" % calctype.upper(),
0,
jobid=form["jobid"].value)
elif progress == "running": # job is not complete, refresh in 30 seconds
print printheader("%s Job Status Page" % calctype.upper(),
refresh,
jobid=form["jobid"].value)
print "<BODY>\n<P>"
print "<h3>Status"
print "</h3>"
print "Message: %s<br />" % progress
print "Run time: %s seconds<br />" % int(runtime)
print "Current time: %s<br />" % time.asctime()
print "</P>\n<HR>\n<P>"
if progress == "complete":
if calctype == "pdb2pqr":
nexturl = 'apbs_cgi.cgi?jobid=%s' % form["jobid"].value
else:
nexturl = 'visualize.cgi?jobid=%s' % form["jobid"].value
if have_opal:
resp = appServicePort.getOutputs(getOutputsRequest(jobid))
filelist = resp._outputFile
print "Here are the results:<ul>"
print "<li>Input files<ul>"
if calctype == "pdb2pqr":
# this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension
if have_opal:
for i in range(0, len(filelist)):
if len(filelist[i]._name) == 4:
print "<li><a href=%s>%s</a></li>" % (
filelist[i]._url, filelist[i]._name)
else:
print "<li><a href=%s%s%s/%s.pdb>%s.pdb</a></li>" % (
WEBSITE, TMPDIR, jobid, jobid, jobid)
elif calctype == "apbs":
if have_opal:
for i in range(0, len(filelist)):
if filelist[i]._name == "apbsinput.in" or filelist[
i]._name[-4:] == ".pqr":
print "<li><a href=%s>%s</a></li>" % (
filelist[i]._url, filelist[i]._name)
else:
print "<li><a href=%s%s%s/apbsinput.in>apbsinput.in</a></li>" % (
WEBSITE, TMPDIR, jobid)
print "<li><a href=%s%s%s/%s.pqr>%s.pqr</a></li>" % (
WEBSITE, TMPDIR, jobid, jobid, jobid)
print "</ul></li>"
print "<li>Output files<ul>"
queryString = [str(os.environ["REMOTE_ADDR"])]
# Getting PDB2PQR run log info
if os.path.isfile('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid)):
pdb2pqrLogFile = open(
'%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid), 'r')
logstr = pdb2pqrLogFile.read().split('\n')
templogopts = eval(logstr[0])
pdb2pqrLogFile.close()
queryString.insert(0, templogopts.get('pdb', ''))
if calctype == "pdb2pqr":
if have_opal:
for i in range(0, len(filelist)):
if filelist[i]._name.endswith(
(".propka", "-typemap.html", ".pqr", ".in")):
# if filelist[i]._name[-4:]==".pqr":
# # Getting pqr file length for PDB2PQR Opal run
# f=urllib.urlopen(filelist[i]._url)
# #pqrOpalFileLength = len(f.readlines())
# f.close()
print "<li><a href=%s>%s</a></li>" % (
filelist[i]._url, filelist[i]._name)
#Get the first line of the summary file.
if filelist[i]._name.endswith(".summary"):
f = urllib.urlopen(filelist[i]._url)
summaryLine = f.readline().strip()
#logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine
queryString.append(summaryLine)
f.close()
# logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR)
else:
#Get the first line of the summary file.
summaryFile = '%s%s%s/%s%s' % (INSTALLDIR, TMPDIR, jobid,
jobid, ".summary")
if os.path.isfile(summaryFile):
with open(summaryFile) as f:
summaryLine = f.readline().strip()
#logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine
queryString.append(summaryLine)
outputfilelist = glob.glob('%s%s%s/*.propka' %
(INSTALLDIR, TMPDIR, jobid))
for i in range(0, len(outputfilelist)):
outputfilelist[i] = os.path.basename(outputfilelist[i])
for extension in ["-typemap.html", ".pqr", ".in"]:
if extension != ".in" or apbs_input != False:
if extension == "-typemap.html" and typemap == False:
continue
outputfilelist.append('%s%s' % (jobid, extension))
for outputfile in outputfilelist:
print "<li><a href=%s%s%s/%s>%s</a></li>" % (
WEBSITE, TMPDIR, jobid, outputfile, outputfile)
logopts['queryPDB2PQR'] = '|'.join(queryString)
#for extension in ["-typemap.html", ".pqr", ".in"]:
# print "<li><a href=%s%s%s/%s%s>%s%s</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, extension, jobid, extension)
elif calctype == "apbs":
if have_opal:
for i in range(0, len(filelist)):
if filelist[i]._name[-3:] == ".dx":
# compressing APBS OpenDX output files
currentpath = os.getcwd()
zipjobid = filelist[i]._name.split("-")[0]
urllib.urlretrieve(
filelist[i]._url, '%s%s%s/%s' %
(INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name))
os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, zipjobid))
# making both the dx file and the compressed file (.gz) available in the directory
syscommand = 'cp %s dxbkupfile' % (filelist[i]._name)
os.system(syscommand)
syscommand = 'gzip -9 ' + filelist[i]._name
os.system(syscommand)
syscommand = 'mv dxbkupfile %s' % (filelist[i]._name)
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = filelist[i]._name + '.gz'
print "<li><a href=%s%s%s/%s>%s</a></li>" % (
WEBSITE, TMPDIR, zipjobid, outputfilezip,
outputfilezip)
else:
outputfilelist = glob.glob('%s%s%s/%s-*.dx' %
(INSTALLDIR, TMPDIR, jobid, jobid))
for outputfile in outputfilelist:
# compressing APBS OpenDX output files
currentpath = os.getcwd()
workingpath = os.path.dirname(outputfile)
os.chdir(workingpath)
# making both the dx file and the compressed file (.gz) available in the directory
syscommand = 'cp %s dxbkupfile' % (
os.path.basename(outputfile))
os.system(syscommand)
syscommand = 'gzip -9 ' + os.path.basename(outputfile)
os.system(syscommand)
syscommand = 'mv dxbkupfile %s' % (
os.path.basename(outputfile))
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = outputfile + ".gz"
print "<li><a href=%s%s%s/%s>%s</a></li>" % (
WEBSITE, TMPDIR, jobid,
os.path.basename(outputfilezip),
os.path.basename(outputfilezip))
logopts['queryAPBS'] = '|'.join(queryString)
print "</ul></li>"
print "<li>Runtime and debugging information<ul>"
if have_opal:
stdouturl = resp._stdOut
stderrurl = resp._stdErr
else:
stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid,
calctype)
stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid,
calctype)
print "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl
print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl
print "</ul></li></ul>"
#if have_opal:
# resp = appServicePort.getOutputs(getOutputsRequest(jobid))
# for opalfile in resp._outputFile:
# if opalfile._name[-8:]!="-input.p":
# print "<li><a href=%s>%s</a></li>" % (opalfile._url, opalfile._name)
# print "<li><a href=%s>Standard output</a></li>" % (resp._stdOut)
# print "<li><a href=%s>Standard error</a></li>" % (resp._stdErr)
#else:
# for line in cp[1:]:
# line = os.path.basename(line)
# if line[-8:]!="-input.p":
# if line[-11:]=="_stdout.txt":
# printname = "Standard output"
# elif line[-11:]=="_stderr.txt":
# printname = "Standard error"
# else:
# printname = line
# print "<li><a href=%s>%s</a></li>" % (WEBSITE+TMPDIR+jobid+"/"+line,printname)
if calctype == "pdb2pqr" and apbs_input and HAVE_APBS != "":
print "</ul></p><hr><p><b><a href=%s>Click here</a> to run APBS with your results.</b></p>" % nexturl
elif calctype == "apbs":
print "</ul></p><hr><p><b><a href=%s>Click here</a> to visualize your results.</b></p>" % nexturl
elif progress == "error":
print "There was an error with your query request. This page will not refresh."
elif progress == "running":
print "Page will refresh in %d seconds<br />" % refresh
print "<HR>"
print "<small>Your results will appear at <a href=%s>this page</a>. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours).</small>" % resultsurl
elif progress == "version_mismatch":
print "The versions of APBS on the local server and on the Opal server do not match, so the calculation could not be completed"
print "</P>"
print "<script type=\"text/javascript\">"
for key in logopts:
print getEventTrackingString('queryData', key, logopts[key]),
#print "_gaq.push(['_trackPageview', '/main_cgi/has_%s_%s.html']);" % (key, logopts[key])
print "</script>"
print "</BODY>"
print "</HTML>"
def main(apbsOptions):
cgiFile = "jmol.cgi"
cgiName = "thisform"
defaultVisType = "jmol"
checkJmolType = True
cssFile = 'pdb2pqr.css'
try:
jobid = form['jobid'].value
tool = form['tool'].value #run 3dmol or jmol
except KeyError:
print redirectString
return
string_3dmol = """
<!DOCTYPE html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<title>Visualization</title>
<link rel="stylesheet" href="3dmol/css/pdb2pqr_3dmol.css" type="text/css">
<link rel="stylesheet" href="3dmol/css/foundation.css">
<link rel="stylesheet" type="text/css" href="3dmol/css/pure-min.css" media="screen" />
<link rel="stylesheet" href="3dmol/css/toggles.css" type="text/css">
<link rel="stylesheet" href="3dmol/css/ui_css.css" type="text/css">
<script type="text/JavaScript" src="3dmol/js/pitt_3Dmol.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
<script src="http://3dmol.csb.pitt.edu/build/3Dmol.js"></script>
<script type="text/JavaScript" src="3dmol/js/visualize_html.js"></script>
<script type="text/JavaScript" src="3dmol/js/3dmol.js"></script>
</head>
<body>
<script type="text/javascript">build_page({jobid})</script>
<script type="text/javascript">getpqr({jobid})</script>
<script type="text/javascript">getcube({jobid})</script>
</body>
</html>""".format(jobid=jobid,
trackingevents=getEventTrackingString(
category='apbs',
action='visualize',
label=str(os.environ["REMOTE_ADDR"])),
trackingscript=getTrackingScriptString(jobid=jobid))
string_jmol = """
<!DOCTYPE html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<title>Visualization</title>
<link rel="stylesheet" href="pdb2pqr.css" type="text/css">
<script type="text/JavaScript" src="jmol/Jmol.js"></script>
<script type="text/JavaScript">APPLET_PATH="jmol/";GZIP=""</script>
<script type="text/JavaScript" src="jmol/apbsjmol.js"></script>
</head>
<body onload="init()">
<script type="text/javascript">createVisualization({jobid}, -5.0, 5.0)</script>
</body>
</html>""".format(jobid=jobid,
trackingevents=getEventTrackingString(
category='apbs',
action='visualize',
label=str(os.environ["REMOTE_ADDR"])),
trackingscript=getTrackingScriptString(jobid=jobid))
if (tool == 'tool_3dmol'):
print string_3dmol
if (tool == 'tool_jmol'):
print string_jmol
def mainCGI():
"""
Main method for determining the query page output
"""
logopts = {}
print "Content-type: text/html\n\n"
calctype = form["calctype"].value
# prints version error, if it exists
if form["jobid"].value == 'False':
print printheader("%s Job Status Page" % calctype.upper())
progress = "version_mismatch"
runtime = 0
elif form["jobid"].value == 'notenoughmem':
print printheader("%s Job Status Page" % calctype.upper())
progress = "not_enough_memory"
runtime = 0
else:
progress = None
#Check for error html
errorpath = '%s%s%s.html' % (INSTALLDIR, TMPDIR, form["jobid"].value)
if os.path.isfile(errorpath):
string = ""
string+= "<html>\n"
string+= "\t<head>\n"
string+= "\t\t<meta http-equiv=\"Refresh\" content=\"0; url=%s%s%s.html\">\n" % (WEBSITE, TMPDIR, form["jobid"].value)
string+= "\t</head>\n"
string+= "</html>\n"
print string
return
# prepares for Opal query, if necessary
if have_opal:
if calctype=="pdb2pqr":
opal_url = PDB2PQR_OPAL_URL
elif calctype=="apbs":
opal_url = APBS_OPAL_URL
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(opal_url)
else:
appServicePort = None
# if PDB2PQR, determines if link to APBS calculation should be shown
if calctype=="pdb2pqr":
#if(form["apbsinput"].value=="True"): # change to use a file
# apbs_input = True
#else:
# apbs_input = False
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, form["jobid"].value))
apbs_input = apbsInputFile.read()
apbsInputFile.close()
if apbs_input=="True":
apbs_input = True
else:
apbs_input = False
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, form["jobid"].value))
typemap = typemapInputFile.read()
typemapInputFile.close()
if typemap=="True":
typemap = True
else:
typemap = False
if have_opal and progress == None:
if form["calctype"].value=="pdb2pqr":
pdb2pqrJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, form["jobid"].value))
jobid = pdb2pqrJobIDFile.read()
pdb2pqrJobIDFile.close()
elif form["calctype"].value=="apbs":
apbsJobIDFile = open('%s%s%s/apbs_opal_job_id' % (INSTALLDIR, TMPDIR, form["jobid"].value))
jobid = apbsJobIDFile.read()
apbsJobIDFile.close()
else:
jobid = form["jobid"].value
if progress == None:
cp = checkprogress(jobid,appServicePort,calctype) # finds out status of job
progress = cp[0]
#initialize with bogus value just in case
starttime = time.time()
if progress == "running" or progress == "complete":
timefile = open('%s%s%s/%s_start_time' % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value))
starttime = float(timefile.read())
timefile.close()
if progress == "running" or (have_opal and progress not in ("version_mismatch",
"not_enough_memory",
"error",
"complete")):
runtime = time.time()-starttime
runtime = int(runtime)
elif progress == "complete":
endTimeFileString = '%s%s%s/%s_end_time' % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value)
if have_opal and not os.path.isfile(endTimeFileString):
runtime = time.time()-starttime
with open(endTimeFileString, 'w') as endTimeFile:
endTimeFile.write(str(time.time()))
else:
with open(endTimeFileString, 'r') as endTimeFile:
runtime = float(endTimeFile.read())-starttime
else:
runtime = -1
if progress == "running":
#if have_opal:
# resultsurl = cp[1]._baseURL
#else:
if calctype=="pdb2pqr":
resultsurl = '%squerystatus.cgi?jobid=%s&apbsinput=%s&calctype=pdb2pqr' % (WEBSITE, form["jobid"].value, apbs_input)
else:
resultsurl = '%squerystatus.cgi?jobid=%s&calctype=apbs' % (WEBSITE, form["jobid"].value)
if progress == "complete":
print printheader("%s Job Status Page" % calctype.upper(), jobid=form["jobid"].value)
elif progress == "error":
print printheader("%s Job Status Page - Error" % calctype.upper(),0, jobid=form["jobid"].value)
elif progress == "running": # job is not complete, refresh in 30 seconds
print printheader("%s Job Status Page" % calctype.upper(), refresh, jobid=form["jobid"].value)
print "<BODY>\n<P>"
print "<p></p>"
print '<div id="content">'
print "<h3>Status:"
color = "FA3434"
image = WEBSITE+"images/red_x.png"
if progress == "complete":
color = "2CDE56"
image = WEBSITE+"images/green_check.png"
elif progress == "running":
color = "ffcc00"
image = WEBSITE+"images/yellow_exclamation.png"
print "<strong style=\"color:#%s;\">%s</strong>" % (color, progress)
print "<img src=\"%s\"><br />" % image
print "</h3>"
print "Run time: " + str(timedelta(seconds=round(runtime))) + '<br />'
print "Current time: %s<br />" % time.asctime()
print "</P>\n<HR>\n<P>"
if progress == "complete":
if calctype=="pdb2pqr":
nexturl = 'apbs_cgi.cgi?jobid=%s' % form["jobid"].value
else:
url_3dmol = 'visualize.cgi?jobid=%s&tool=%s' % (form["jobid"].value,'tool_3dmol')
url_jmol = 'visualize.cgi?jobid=%s&tool=%s' % (form["jobid"].value,'tool_jmol')
if have_opal:
resp = appServicePort.getOutputs(getOutputsRequest(jobid))
filelist = resp._outputFile
print "Here are the results:<ul>"
print "<li>Input files<ul>"
if calctype=="pdb2pqr":
# this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension
if have_opal:
for i in range(0,len(filelist)):
file_name = filelist[i]._name
if ((len(file_name) == 4 and '.' not in file_name) or
(file_name.lower().endswith(".pdb") and "pdb2pka_output" not in file_name)):
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
if file_name.lower().endswith((".mol", ".mol2", ".names", ".dat")) and "pdb2pka_output" not in file_name:
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
else:
print "<li><a href=%s%s%s/%s.pdb>%s.pdb</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, jobid)
elif calctype=="apbs":
if have_opal:
for i in range(0,len(filelist)):
if filelist[i]._name == "apbsinput.in" or filelist[i]._name[-4:] == ".pqr":
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
else:
print "<li><a href=%s%s%s/apbsinput.in>apbsinput.in</a></li>" % (WEBSITE, TMPDIR, jobid)
print "<li><a href=%s%s%s/%s.pqr>%s.pqr</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, jobid)
print "</ul></li>"
print "<li>Output files<ul>"
queryString = [str(os.environ["REMOTE_ADDR"])]
# Getting PDB2PQR run log info
if os.path.isfile('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid)):
pdb2pqrLogFile=open('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid), 'r')
logstr=pdb2pqrLogFile.read().split('\n')
templogopts = eval(logstr[0])
pdb2pqrLogFile.close()
queryString.insert(0, templogopts.get('pdb',''))
if calctype=="pdb2pqr":
if have_opal:
for i in range(0,len(filelist)):
if filelist[i]._name.endswith((".propka", "-typemap.html")):
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
if filelist[i]._name.endswith(".in") and "pdb2pka_output" not in filelist[i]._name:
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
if filelist[i]._name.endswith(".pqr") and not filelist[i]._name.endswith("background_input.pqr"):
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
#Get the first line of the summary file.
if filelist[i]._name.endswith(".summary"):
f=urllib.urlopen(filelist[i]._url)
summaryLine = f.readline().strip()
#logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine
queryString.append(summaryLine)
f.close()
# logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR)
else:
#Get the first line of the summary file.
summaryFile = '%s%s%s/%s%s' % (INSTALLDIR, TMPDIR, jobid, jobid, ".summary")
if os.path.isfile(summaryFile):
with open(summaryFile) as f:
summaryLine = f.readline().strip()
#logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine
queryString.append(summaryLine)
outputfilelist = glob.glob('%s%s%s/*.propka' % (INSTALLDIR, TMPDIR, jobid))
for i in range(0,len(outputfilelist)):
outputfilelist[i] = os.path.basename(outputfilelist[i])
for extension in ["-typemap.html", ".pqr", ".in"]:
if extension != ".in" or apbs_input != False:
if extension == "-typemap.html" and typemap == False:
continue
outputfilelist.append('%s%s' % (jobid, extension))
for outputfile in outputfilelist:
print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, outputfile, outputfile)
logopts['queryPDB2PQR'] = '|'.join(queryString)
#for extension in ["-typemap.html", ".pqr", ".in"]:
# print "<li><a href=%s%s%s/%s%s>%s%s</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, extension, jobid, extension)
elif calctype=="apbs":
if have_opal:
for i in range(0,len(filelist)):
if filelist[i]._name[-3:]==".dx":
# compressing APBS OpenDX output files
currentpath = os.getcwd()
zipjobid = filelist[i]._name.split("-")[0]
dxfilename = '%s%s%s/%s' % (INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name)
urllib.urlretrieve(filelist[i]._url, dxfilename)
os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, zipjobid))
# making both the dx file and the compressed file (.gz) available in the directory
syscommand = 'cp %s dxbkupfile' % (filelist[i]._name)
os.system(syscommand)
syscommand = 'gzip -9 ' + filelist[i]._name
os.system(syscommand)
syscommand = 'mv dxbkupfile %s' % (filelist[i]._name)
os.system(syscommand)
outputfilezip = filelist[i]._name + '.gz'
pqrfilename = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, zipjobid, zipjobid)
cubefilename = '%s%s%s/%s.cube' % (INSTALLDIR, TMPDIR, zipjobid, zipjobid)
# making both the cube file and the compressed file (.gz) available in the directory
createcube(dxfilename, pqrfilename, cubefilename)
cubefilebasename = os.path.basename(cubefilename)
syscommand = 'cp %s cubebkupfile' % cubefilebasename
os.system(syscommand)
syscommand = 'gzip -9 ' + cubefilebasename
os.system(syscommand)
syscommand = 'mv cubebkupfile %s' % cubefilebasename
os.system(syscommand)
os.chdir(currentpath)
outputcubefilezip = cubefilebasename+".gz"
print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, zipjobid, outputfilezip, outputfilezip)
print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, zipjobid, outputcubefilezip, outputcubefilezip)
else:
outputfilelist = glob.glob('%s%s%s/%s-*.dx' % (INSTALLDIR, TMPDIR, jobid, jobid))
for dxfile in outputfilelist:
# compressing APBS OpenDX output files
currentpath = os.getcwd()
workingpath = os.path.dirname(dxfile)
os.chdir(workingpath)
# making both the dx file and the compressed file (.gz) available in the directory
syscommand = 'cp %s dxbkupfile' % (os.path.basename(dxfile))
os.system(syscommand)
syscommand = 'gzip -9 ' + os.path.basename(dxfile)
os.system(syscommand)
syscommand = 'mv dxbkupfile %s' % (os.path.basename(dxfile))
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = dxfile+".gz"
cubefilename = '%s%s%s/%s.cube' % (INSTALLDIR, TMPDIR, jobid, jobid)
pqrfilename = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, jobid, jobid)
createcube(dxfile, pqrfilename, cubefilename)
print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, os.path.basename(outputfilezip), os.path.basename(outputfilezip))
outputcubefilelist = glob.glob('%s%s%s/%s.cube' % (INSTALLDIR, TMPDIR, jobid, jobid))
for cubefile in outputcubefilelist:
# compressing cube output file
currentpath = os.getcwd()
os.chdir(workingpath)
# making both the cube file and the compressed file (.gz) available in the directory
syscommand = 'cp %s cubebkupfile' % (os.path.basename(cubefile))
os.system(syscommand)
syscommand = 'gzip -9 ' + os.path.basename(cubefile)
os.system(syscommand)
syscommand = 'mv cubebkupfile %s' % (os.path.basename(cubefile))
os.system(syscommand)
os.chdir(currentpath)
outputcubefilezip = cubefile+".gz"
print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, os.path.basename(outputcubefilezip), os.path.basename(outputcubefilezip))
logopts['queryAPBS'] = '|'.join(queryString)
if calctype=="pdb2pqr":
if have_opal:
outputfilelist = []
for i in range(0,len(filelist)):
if filelist[i]._name.endswith((".DAT", ".txt")):
outputfilelist.append((filelist[i]._url, os.path.basename(filelist[i]._name)))
#print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
if outputfilelist:
print "</ul></li>"
print "<li>PDB2PKA files<ul>"
for outputfile in outputfilelist:
print "<li><a href=%s>%s</a></li>" % (outputfile[0], outputfile[1])
else:
outputfilelist = glob.glob('%s%s%s/pdb2pka_output/*.DAT' % (INSTALLDIR, TMPDIR, jobid))
outputfilelist.extend(glob.glob('%s%s%s/pdb2pka_output/*.txt' % (INSTALLDIR, TMPDIR, jobid)))
outputfilelist = [os.path.basename(outputfile) for outputfile in outputfilelist]
if outputfilelist:
print "</ul></li>"
print "<li>PDB2PKA files<ul>"
for outputfile in outputfilelist:
print "<li><a href=%s%s%s/pdb2pka_output/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, outputfile, outputfile)
print "</ul></li>"
print "<li>Runtime and debugging information<ul>"
if have_opal:
stdouturl = resp._stdOut
stderrurl = resp._stdErr
else:
stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid, calctype)
stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid, calctype)
print "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl
print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl
print "</ul></li></ul>"
#if have_opal:
# resp = appServicePort.getOutputs(getOutputsRequest(jobid))
# for opalfile in resp._outputFile:
# if opalfile._name[-8:]!="-input.p":
# print "<li><a href=%s>%s</a></li>" % (opalfile._url, opalfile._name)
# print "<li><a href=%s>Standard output</a></li>" % (resp._stdOut)
# print "<li><a href=%s>Standard error</a></li>" % (resp._stdErr)
#else:
# for line in cp[1:]:
# line = os.path.basename(line)
# if line[-8:]!="-input.p":
# if line[-11:]=="_stdout.txt":
# printname = "Standard output"
# elif line[-11:]=="_stderr.txt":
# printname = "Standard error"
# else:
# printname = line
# print "<li><a href=%s>%s</a></li>" % (WEBSITE+TMPDIR+jobid+"/"+line,printname)
if calctype=="pdb2pqr" and apbs_input and HAVE_APBS:
print "</ul></p><hr><p><b><a href=%s>Click here</a> to run APBS with your results.</b></p>" % nexturl
elif calctype=="apbs":
#print "</ul></p><hr><p><b><a href=%s>Click here</a> to visualize your results in Jmol.</b></p>" % nexturl
print "</ul></p><hr><p><b>Visualize your results online:"
print "<ul> <li><a href=%s>3Dmol</a></li><li><a href=%s>Jmol</a></li></ul>" % (url_3dmol, url_jmol)
elif progress == "error":
print "There was an error with your query request. This page will not refresh."
print "</ul></li>"
print "<li>Runtime and debugging information<ul>"
if have_opal:
resp = appServicePort.getOutputs(getOutputsRequest(jobid))
stdouturl = resp._stdOut
stderrurl = resp._stdErr
else:
stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid, calctype)
stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid, calctype)
print "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl
print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl
print "</ul></li></ul>"
if have_opal:
print " <br />If your job has been running for a prolonged period of time and failed with no reason listed in the standard out or standard error, then the job probably timed out and was terminated by the system.<br />"
print '<br />If you are having trouble running PDB2PQR on the webserver, please download the <a href="http://www.poissonboltzmann.org/docs/downloads/">command line version of PDB2PQR</a> and run the job from there.'
elif progress == "running":
print "Page will refresh in %d seconds<br />" % refresh
print "<HR>"
if not have_opal:
print "</ul></li>"
print "<li>Runtime and debugging information<ul>"
stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid, calctype)
stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid, calctype)
print "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl
print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl
print "</ul></li></ul>"
print "<small>Your results will appear at <a href=%s>this page</a>. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours).</small>" % resultsurl
elif progress == "version_mismatch":
print "The versions of APBS on the local server and on the Opal server do not match, so the calculation could not be completed"
print "</P>"
print "<script type=\"text/javascript\">"
for key in logopts:
print getEventTrackingString('queryData', key, logopts[key]),
#print "_gaq.push(['_trackPageview', '/main_cgi/has_%s_%s.html']);" % (key, logopts[key])
print "</script>"
print "</div> <!--end content div-->"
print "</BODY>"
print "</HTML>"
def main(apbsOptions):
cgiFile = "jmol.cgi"
cgiName = "thisform"
defaultVisType = "jmol"
checkJmolType = True
cssFile = 'pdb2pqr.css'
try:
jobid = form['jobid'].value
tool = form['tool'].value #run 3dmol or jmol
except KeyError:
print redirectString
return
string_3dmol = """
<!DOCTYPE html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<title>Visualization</title>
<link rel="stylesheet" href="3dmol/css/pdb2pqr_3dmol.css" type="text/css">
<link rel="stylesheet" href="3dmol/css/foundation.css">
<link rel="stylesheet" type="text/css" href="3dmol/css/pure-min.css" media="screen" />
<link rel="stylesheet" href="3dmol/css/toggles.css" type="text/css">
<link rel="stylesheet" href="3dmol/css/ui_css.css" type="text/css">
<script type="text/JavaScript" src="3dmol/js/pitt_3Dmol.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
<script src="http://3dmol.csb.pitt.edu/build/3Dmol.js"></script>
<script type="text/JavaScript" src="3dmol/js/visualize_html.js"></script>
<script type="text/JavaScript" src="3dmol/js/3dmol.js"></script>
</head>
<body>
<script type="text/javascript">build_page({jobid})</script>
<script type="text/javascript">getpqr({jobid})</script>
<script type="text/javascript">getcube({jobid})</script>
</body>
</html>""".format(jobid=jobid,
trackingevents=getEventTrackingString(category='apbs',
action='visualize',
label=str(os.environ["REMOTE_ADDR"])),
trackingscript=getTrackingScriptString(jobid=jobid))
string_jmol = """
<!DOCTYPE html>
<head>
{trackingscript}
<script type="text/javascript">
{trackingevents}
</script>
<title>Visualization</title>
<link rel="stylesheet" href="pdb2pqr.css" type="text/css">
<script type="text/JavaScript" src="jmol/Jmol.js"></script>
<script type="text/JavaScript">APPLET_PATH="jmol/";GZIP=""</script>
<script type="text/JavaScript" src="jmol/apbsjmol.js"></script>
</head>
<body onload="init()">
<script type="text/javascript">createVisualization({jobid}, -5.0, 5.0)</script>
</body>
</html>""".format(jobid=jobid,
trackingevents=getEventTrackingString(category='apbs',
action='visualize',
label=str(os.environ["REMOTE_ADDR"])),
trackingscript=getTrackingScriptString(jobid=jobid))
if(tool == 'tool_3dmol'):
print string_3dmol
if(tool == 'tool_jmol'):
print string_jmol
def redirector(name, weboptions, jobtype=None, client_ip=None, analytics_id=None, ga_client_id=None):
"""
Prints a page which redirects the user to querystatus.cgi and writes starting time to file
"""
redirectWait = 3
utilities.startLogFile(name, 'pdb2pqr_start_time', str(time.time()))
jobtype_query = ''
if jobtype is not None:
jobtype_query = '&jobtype=%s' % jobtype
jobid = name
if weboptions is None:
ui_url = os.getenv("UI_URL", "http://localhost:3000")
redirectURL = "{website}jobstatus?jobid={jobid}{jobtype}".format(website=ui_url, jobid=jobid, jobtype=jobtype_query)
else:
analiticsDict = weboptions.getOptions()
events = {}
if client_ip is not None:
events['submission'] = analiticsDict['pdb']+'|'+str(client_ip)
else:
events['submission'] = analiticsDict['pdb']+'|'+str(None)
# events['submission'] = analiticsDict['pdb']+'|'+str(os.environ["REMOTE_ADDR"])
del analiticsDict['pdb']
events['titration'] = str(analiticsDict.get('ph'))
if 'ph' in analiticsDict:
del analiticsDict['ph']
events['apbsInput'] = str(analiticsDict.get('apbs'))
del analiticsDict['apbs']
#Clean up selected extensions output
if 'selectedExtensions' in analiticsDict:
analiticsDict['selectedExtensions'] = ' '.join(analiticsDict['selectedExtensions'])
options = ','.join(str(k)+':'+str(v) for k,v in analiticsDict.iteritems())
events['options']=options
eventsScriptString = ''
for event in events:
eventsScriptString += utilities.getEventTrackingString(category='submissionData',
action=event,
label=events[event])
logging.debug('analytics_id: %s', analytics_id)
ga_event_request_body = ''
if analytics_id is not None:
ga_event_request_body = ''
ga_event_headers = {
'User-Agent': request.headers['User-Agent']
}
on_first = True
for event in events:
# Make Google Analytics request body
ga_event_request_body += 'v=1&tid=%s&cid=%s&t=event&ec=submissionData&ea=%s&el=%s\n' % (analytics_id, ga_client_id, event, events[event])
try:
logging.info('GA request body:\n%s' % ga_event_request_body)
logging.info('Sending usage data through Google Analytics endpoint')
r = requests.post('https://www.google-analytics.com/batch', data=ga_event_request_body, headers=ga_event_headers)
if not r.ok:
r.raise_for_status()
except Exception as err:
raise
redirectURL = "{website}jobstatus?jobid={jobid}{jobtype}".format(website=WEBSITE, jobid=jobid, jobtype=jobtype_query)
# string = """
# <html>
# <head>
# {trackingscript}
# <script type="text/javascript">
# {trackingevents}
# </script>
# <meta http-equiv="Refresh" content="{wait}; url={redirectURL}">
# <link rel="stylesheet" href="{website}pdb2pqr.css"type="text/css">
# </head>
# <body>
# <center>
# You are being automatically redirected to a new location.<br />
# If your browser does not redirect you in {wait} seconds, or you do
# not wish to wait, <a href="{redirectURL}">click here</a></center>.
# </body>
# </html>""".format(trackingscript=utilities.getTrackingScriptString(jobid=jobid),
# trackingevents=eventsScriptString, redirectURL=redirectURL, wait=redirectWait, website=WEBSITE)
# return string
return redirectURL
