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 printheader(pagetitle, refresh=None, jobid=None):
str = ""
str += "<html>\n"
str += "<HEAD>\n"
if refresh:
str += "\t<META HTTP-EQUIV=\"Refresh\" CONTENT=\"%s\">\n" % refresh
str += "\t<TITLE>%s</TITLE>\n" % pagetitle
str += "\t<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % STYLESHEET
str += getTrackingScriptString(jobid)
str += "</HEAD>\n"
return str
def printheader(pagetitle,refresh=None,jobid=None):
str = ""
str+= "<html>\n"
str+= "<HEAD>\n"
if refresh:
str+= "\t<META HTTP-EQUIV=\"Refresh\" CONTENT=\"%s\">\n" % refresh
str+= "\t<TITLE>%s</TITLE>\n" % pagetitle
str+= "\t<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % STYLESHEET
str+= getTrackingScriptString(jobid)
str+= "</HEAD>\n"
return str
def printheader(pagetitle,refresh=None,jobid=None):
str = ""
str+= "<html>\n"
str+= "<HEAD>\n"
str+= '<img src="https://raw.githubusercontent.com/Electrostatics/apbs-pdb2pqr/master/apbs/doc/icons/APBS_128_v2.png" style="float:right; position:relative;right:200px; top: 2px;">'
if refresh:
str+= "\t<META HTTP-EQUIV=\"Refresh\" CONTENT=\"%s\">\n" % refresh
str+= "\t<TITLE>%s</TITLE>\n" % pagetitle
str+= "\t<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % STYLESHEET
str+= getTrackingScriptString(jobid)
str+= "</HEAD>\n"
return str
def printheader(pagetitle, refresh=None, jobid=None):
str = ""
str += "<html>\n"
str += "<HEAD>\n"
str += '<img src="https://raw.githubusercontent.com/Electrostatics/apbs-pdb2pqr/master/apbs/doc/icons/APBS_128_v2.png" style="float:right; position:relative;right:200px; top: 2px;">'
if refresh:
str += "\t<META HTTP-EQUIV=\"Refresh\" CONTENT=\"%s\">\n" % refresh
str += "\t<TITLE>%s</TITLE>\n" % pagetitle
str += "\t<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % STYLESHEET
str += getTrackingScriptString(jobid)
str += "</HEAD>\n"
return str
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 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 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