#!@WHICHPYTHON@
"""
CGI Module for checking on the status of an OPAL job
"""
__date__ = "4 January 2010"
__author__ = "Wes Goodman, Samir Unni, Yong Huang"
import sys
import cgi
import cgitb
import os,shutil,glob,string,time,urllib
from datetime import timedelta
from src.server import *
from src.aconf import *
from src.utilities import getTrackingScriptString, getEventTrackingString
cgitb.enable()
form = cgi.FieldStorage()
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 createcube(dx_input, pqr_input, output):
with open(dx_input, 'r') as in_f, open(output, 'w') as out_f, open(pqr_input, 'r') as in_pqr:
out_f.write("CPMD CUBE FILE.\n"
"OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n")
#Discard comments at top of file.
line = in_f.readline()
newline = in_pqr.readline()
while line.startswith('#'):
line = in_f.readline()
split_line = line.split()
grid_sizes = [int(x)*-1 for x in split_line[-3:]]
split_line = in_f.readline().split()
origin = [float(x) for x in split_line[-3:]]
parameter_fmt = "{:>4} {:>11.6f} {:>11.6f} {:>11.6f}\n"
atom_num = 0
while newline.startswith('REMARK'):
newline = in_pqr.readline()
try:
while newline.startswith('ATOM') or newline.startswith('HETATM'):
newline = in_pqr.readline()
new_split_line = newline.split()
atom_num = new_split_line[1]
except IndexError:
pass
in_pqr.seek(0)
newline = in_pqr.readline()
while newline.startswith('REMARK'):
newline = in_pqr.readline()
origin_line = parameter_fmt.format(atom_num, *origin)
out_f.write(origin_line)
for x in xrange(3):
split_line = in_f.readline().split()
grid_dims = [float(item) for item in split_line[-3:]]
dim_lin = parameter_fmt.format(grid_sizes[x], *grid_dims)
out_f.write(dim_lin)
atoms_parameter_fmt = "{:>4} {:>11.6f} {:>11.6f} {:>11.6f} {:>11.6f}\n"
a = True
xreal_center = []
yreal_center = []
zreal_center = []
try:
while newline.startswith('ATOM') or newline.startswith('HETATM'):
new_split_line = newline.split()
radius = new_split_line[-1]
xyz = new_split_line[-5:-2]
line_atom_num = new_split_line[1]
atom_radius = new_split_line[-1]
pqr_lin = atoms_parameter_fmt.format(int(line_atom_num), float(new_split_line[-2]), float(xyz[0]), float(xyz[1]), float(xyz[2]))
out_f.write(pqr_lin)
newline = in_pqr.readline()
xreal_center.append(float(xyz[0]))
yreal_center.append(float(xyz[1]))
zreal_center.append(float(xyz[2]))
except IndexError:
pass
x_avg = sum(xreal_center)/float(atom_num)
y_avg = sum(yreal_center)/float(atom_num)
z_avg = sum(zreal_center)/float(atom_num)
#print origin
#new_origin = []
#for item in origin:
# newitem = item/0.529177
#new_new = item/2 + newitem/2
# new_origin.append(newitem)
#print new_origin
#Consume unneeded object lines.
in_f.readline()
in_f.readline()
##TODO: put atoms here
value_format = ["{:< 13.5E}"]
value_format = ' '.join(value_format * 6) + '\n'
group = []
line = in_f.readline()
while not line.startswith('attribute'):
values = [float(item) for item in line.split()]
group.extend(values)
if len(group) >= 6:
out_f.write(value_format.format(*group))
group = []
line = in_f.readline()
if group:
group_strs = ["{:< 13.5E}".format(item) for item in group]
out_f.write(' '.join(group_strs))
def checkprogress(jobid=None,appServicePort=None,calctype=None):
"""
Finds out if the job has been completed
"""
if have_opal:
# construct soap request
try:
status=appServicePort.queryStatus(queryStatusRequest(jobid))
except Exception, e:
return ["error"]
if status._code == 4:
return ["error"]
if status._code == 8:
return ["complete",status]
else:
return ["running",status]
else:
progress = []
file = open('%s%s%s/%s_status' % (INSTALLDIR,TMPDIR,jobid, form["calctype"].value))
for line in file.readlines():
progress.append(string.strip(line))
file.close()
return progress
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>"
if __name__ == "__main__" and os.environ.has_key("REQUEST_METHOD"):
""" Determine if called from command line or CGI """
refresh=30
if not form.has_key("jobid") and form["calctype"].value=="pdb2pqr":
print "Content-type: text/html\n\n"
print printheader("PDB2PQR Job Status - Error")
text="<BODY>\n"
text+="\t<H2>Missing jobid field</H2>\n"
text+="\t<P>Your request url is missing the jobid field</P>\n"
text += "<script type=\"text/javascript\">"
text += "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
text += "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
text += "</script>"
text += "<script type=\"text/javascript\">"
text += "try {"
text += "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text+="</BODY>\n</HTML>"
print text
sys.exit(2)
if (form["calctype"].value=="pdb2pqr" and HAVE_PDB2PQR_OPAL) or (form["calctype"].value=="apbs" and APBS_OPAL_URL!=""):
have_opal = True
from AppService_client import AppServiceLocator, queryStatusRequest, getOutputsRequest
else:
have_opal = False
mainCGI()