def getOutputFiles(self):
""" it returns a list of strings containing the URLs of the output files
produced by the job """
resp = self.opalService.appServicePort.getOutputs(getOutputsRequest(self.jobID))
outputFile = []
for i in resp._outputFile:
outputFile.append(i._url)
return outputFile
def getOutputs(self):
if self.status is None:
raise RuntimeError("No job has been launched yet")
from AppService_client import getOutputsRequest
import socket
req = getOutputsRequest(self.jobID)
try:
resp = self.appServicePort.getOutputs(req)
except socket.error, e:
from chimera import NonChimeraError
raise NonChimeraError(str(e))
def getOutputs(self):
if self.status is None:
raise RuntimeError("No job has been launched yet")
from AppService_client import getOutputsRequest
import socket
req = getOutputsRequest(self.jobID)
try:
resp = self.appServicePort.getOutputs(req)
except socket.error, e:
from chimera import NonChimeraError
raise NonChimeraError(str(e))
def displayResults(jobID):
""" Displays URLs of resulting files, if they are not to be fetched automatically. """
global service_url
appServicePort = AppServiceLocator().getAppServicePort(service_url)
resp = appServicePort.getOutputs(getOutputsRequest(jobID))
# Retrieve a listing of all output files
stdout.write("\tStandard Output: %s\n" % resp._stdOut, "\n")
stdout.write("\tStandard Error: %s\n", resp._stdErr)
if (resp._outputFile != None):
for i in range(0, resp._outputFile.__len__()):
stdout.write("\t%s: %s\n" % (resp._outputFile[i]._name, resp._outputFile[i]._url))
stdout.write("\tStandard Error: %s\n" % resp._stdErr)
def displayResults(jobID):
""" Displays URLs of resulting files, if they are not to be fetched automatically. """
global service_url
appServicePort = AppServiceLocator().getAppServicePort(service_url)
resp = appServicePort.getOutputs(getOutputsRequest(jobID))
# Retrieve a listing of all output files
stdout.write("\tStandard Output: %s\n" % resp._stdOut, "\n")
stdout.write("\tStandard Error: %s\n", resp._stdErr)
if (resp._outputFile != None):
for i in range(0, resp._outputFile.__len__()):
stdout.write("\t%s: %s\n" %
(resp._outputFile[i]._name, resp._outputFile[i]._url))
stdout.write("\tStandard Error: %s\n" % resp._stdErr)
def pollStatus(jobID,outputDirectory):
""" Determines current status of run and executes fetching of results if the run is completed. """
global service_url
appServicePort = AppServiceLocator().getAppServicePort(service_url)
status = appServicePort.queryStatus(queryStatusRequest(jobID))
if status._code == 4:
stderr.write("Error! The calculation failed!\n")
stderr.write("Message: %s\n" % status._message)
sys.exit(13)
elif status._code != 8:
stderr.write("Sorry, the calculation hasn't been completed yet. Please wait a short while and attempt to fetch the files again.\n")
sys.exit(13)
else:
resp = appServicePort.getOutputs(getOutputsRequest(jobID))
fetchResults(jobID, outputDirectory, resp._outputFile, status._code==4)
def pollStatus(jobID, outputDirectory):
""" Determines current status of run and executes fetching of results if the run is completed. """
global service_url
appServicePort = AppServiceLocator().getAppServicePort(service_url)
status = appServicePort.queryStatus(queryStatusRequest(jobID))
if status._code == 4:
stderr.write("Error! The calculation failed!\n")
stderr.write("Message: %s\n" % status._message)
sys.exit(13)
elif status._code != 8:
stderr.write(
"Sorry, the calculation hasn't been completed yet. Please wait a short while and attempt to fetch the files again.\n"
)
sys.exit(13)
else:
resp = appServicePort.getOutputs(getOutputsRequest(jobID))
fetchResults(jobID, outputDirectory, resp._outputFile,
status._code == 4)
def initVars():
#global serviceURL
if not form.has_key("jobid"):
pass # add code to redirect to PDB2PQR input page here
else:
jobid = form['jobid'].value
#aspFile = open('./tmp/%s/%s-asp' % (logTime, logTime))
#appServicePort = pickle.load(aspFile)
#aspFile.close()
#jobInfoFile = open('./tmp/%s/%s-jobinfo' % (logTime, logTime))
#jobID = jobInfoFile.read()
#jobInfoFile.close()
aoFile = open('%s%s%s/%s-ao' % (INSTALLDIR, TMPDIR, jobid, jobid))
apbsOptions = pickle.load(aoFile)
aoFile.close()
if APBS_OPAL_URL != "":
from AppService_client import AppServiceLocator, getOutputsRequest
apbsOpalJobIDFile = open('%s%s%s/apbs_opal_job_id' %
(INSTALLDIR, TMPDIR, jobid))
apbsOpalJobID = apbsOpalJobIDFile.read()
apbsOpalJobIDFile.close()
appLocator = AppServiceLocator()
resp = appLocator.getAppServicePort(APBS_OPAL_URL).getOutputs(
getOutputsRequest(apbsOpalJobID))
if not os.access('%s%s%s' % (INSTALLDIR, TMPDIR, jobid), os.F_OK):
os.mkdir('%s%s%s' % (INSTALLDIR, TMPDIR, jobid))
for file in resp._outputFile:
fileName = file._name
if fileName != "Standard Output" and fileName != "Standard Error":
urllib.urlretrieve(
file._url,
'%s%s%s/%s' % (INSTALLDIR, TMPDIR, jobid, fileName))
return apbsOptions
def initVars():
#global serviceURL
if not form.has_key("jobid"):
pass # add code to redirect to PDB2PQR input page here
else:
jobid = form['jobid'].value
#aspFile = open('./tmp/%s/%s-asp' % (logTime, logTime))
#appServicePort = pickle.load(aspFile)
#aspFile.close()
#jobInfoFile = open('./tmp/%s/%s-jobinfo' % (logTime, logTime))
#jobID = jobInfoFile.read()
#jobInfoFile.close()
aoFile = open('%s%s%s/%s-ao' % (INSTALLDIR, TMPDIR, jobid, jobid))
apbsOptions = pickle.load(aoFile)
aoFile.close()
if APBS_OPAL_URL!="":
from AppService_client import AppServiceLocator, getOutputsRequest
apbsOpalJobIDFile = open('%s%s%s/apbs_opal_job_id' % (INSTALLDIR, TMPDIR, jobid))
apbsOpalJobID = apbsOpalJobIDFile.read()
apbsOpalJobIDFile.close()
appLocator = AppServiceLocator()
resp = appLocator.getAppServicePort(APBS_OPAL_URL).getOutputs(getOutputsRequest(apbsOpalJobID))
if not os.access('%s%s%s' % (INSTALLDIR, TMPDIR, jobid), os.F_OK):
os.mkdir('%s%s%s' % (INSTALLDIR, TMPDIR, jobid))
for file in resp._outputFile:
fileName = file._name
if fileName!="Standard Output" and fileName!="Standard Error":
urllib.urlretrieve(file._url, '%s%s%s/%s' % (INSTALLDIR, TMPDIR, jobid, fileName))
return apbsOptions
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>"
print "Waiting 30 seconds" sleep(30) # Query job status status = appServicePort.queryStatus(queryStatusRequest(jobID)) # If execution is successful retrieve job outputs. if status._code == 8: # 8 = GramJob.STATUS_DONE # Create local directory to hold output files output_dir = 'meme_out' mkdir(output_dir); # Instantiate a collection of outputs outputs = appServicePort.getOutputs(getOutputsRequest(jobID)) # Instantiate a request object for retrieving output files fileRequest = getOutputAsBase64ByNameRequest() # Retreive each output file and save to local directory. # MEME writes stdout and stderr to files that aren't listed # in the response, so we handle those separately. print "\tStandard Output:", outputs._stdOut localOutput = open(output_dir + '/' + "stdout.txt", "w") fileRequest._jobID = jobID fileRequest._fileName = "stdout.txt" content = appServicePort.getOutputAsBase64ByName(fileRequest) print >>localOutput, content localOutput.close() print "\tStandard Error:", outputs._stdErr
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 != "version_mismatch" and progress != "not_enough_memory" and progress != "error"
):
runtime = time.time() - starttime
elif progress == "complete":
endtimefile = open("%s%s%s/%s_end_time" % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value))
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())
elif progress == "error":
print printheader("%s Job Status Page - Error" % calctype.upper(), 0)
elif progress == "running": # job is not complete, refresh in 30 seconds
print printheader("%s Job Status Page" % calctype.upper(), refresh)
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>"
if calctype == "pdb2pqr":
if have_opal:
# Getting PDB2PQR Opal run log info
if os.path.isfile("%s%s%s/pdb2pqr_opal_log" % (INSTALLDIR, TMPDIR, form["jobid"].value)):
pdb2pqrOpalLogFile = open(
"%s%s%s/pdb2pqr_opal_log" % (INSTALLDIR, TMPDIR, form["jobid"].value), "r"
)
logstr = pdb2pqrOpalLogFile.read().split("\n")
logopts = eval(logstr[0])
# logff = logstr[1]
# REMOTE_ADDR = logstr[2]
pdb2pqrOpalLogFile.close()
for i in range(0, len(filelist)):
if (
filelist[i]._name[-7:] == ".propka"
or (filelist[i]._name[-13:] == "-typemap.html" and typemap == True)
or filelist[i]._name[-4:] == ".pqr"
or filelist[i]._name[-3:] == ".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)
# logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR)
else:
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)
# 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),
)
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><a href=%s>Click here</a> to run APBS with your results.</p>" % nexturl
elif calctype == "apbs":
print "</ul></p><hr><p><a href=%s>Click here</a> to visualize your results.</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">'
print 'var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");'
print "document.write(unescape(\"%3Cscript src='\" + gaJsHost + \"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E\"));"
print "</script>"
print '<script type="text/javascript">'
print "try {"
print 'var pageTracker = _gat._getTracker("UA-11026338-3");'
if logopts != {}:
for key in logopts:
print 'pageTracker._trackPageview("/main_cgi/has_%s_%s.html");' % (key, logopts[key])
print "pageTracker._trackPageview();"
print "} catch(err) {}</script>"
print "</BODY>"
print "</HTML>"
print "Waiting 30 seconds"
sleep(30)
# Query job status
status = appServicePort.queryStatus(queryStatusRequest(jobID))
# If execution is successful retrieve job outputs.
if status._code == 8: # 8 = GramJob.STATUS_DONE
# Create local directory to hold output files
output_dir = "meme_out"
mkdir(output_dir)
# Instantiate a collection of outputs
outputs = appServicePort.getOutputs(getOutputsRequest(jobID))
# Instantiate a request object for retrieving output files
fileRequest = getOutputAsBase64ByNameRequest()
# Retreive each output file and save to local directory.
# MEME writes stdout and stderr to files that aren't listed
# in the response, so we handle those separately.
print "\tStandard Output:", outputs._stdOut
localOutput = open(output_dir + "/" + "stdout.txt", "w")
fileRequest._jobID = jobID
fileRequest._fileName = "stdout.txt"
content = appServicePort.getOutputAsBase64ByName(fileRequest)
print >> localOutput, content
localOutput.close()
print "\tStandard Error:", outputs._stdErr
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 ws_compute(self):
if self._port_list[0][3]['url'] != None:
url = self._port_list[0][3]['url']
adv = self._port_list[0][3]['adv']
else:
url = ""
print "ERROR: There are no input arguments provided for this web service"
cmdline = ""
numProcs = None
tagged = []
untagged = []
flags = []
files = []
for i in self._port_list:
pn = i[0]
meta = i[3]
if ((self.hasInputFromPort(pn) and self.getInputFromPort(pn) != "") or meta['default'] != None) and adv == True:
# print "META"
# print meta
if meta['type'] == 'FLAG':
if self.hasInputFromPort(pn):
if self.getInputFromPort(pn) == True:
flags.append(meta['arg'])
elif meta['default'] == 'True':
flags.append(meta['arg'])
elif meta['type'] == 'TAGGED':
if self.hasInputFromPort(pn):
val = self.getInputFromPort(pn)
elif meta['default'] != None:
val = meta['default']
if meta['file'] == True:
file_an = core.modules.basic_modules.File.translate_to_string(val)
file_bn = os.path.basename(file_an)
tagged.append(meta['arg'] + file_bn)
files.append(file_an)
else:
tagged.append(meta['arg'] + val)
elif meta['type'] == 'UNTAGGED':
if self.hasInputFromPort(pn):
val = self.getInputFromPort(pn)
elif meta['default'] != None:
val = meta['default']
if meta['file'] == True:
file_an = core.modules.basic_modules.File.translate_to_string(val)
file_bn = os.path.basename(file_an)
untagged.append(file_bn)
files.append(file_an)
else:
untagged.append(val)
cmdline = ""
for i in flags:
cmdline += i + " "
for i in tagged:
cmdline += i + " "
for i in untagged:
cmdline += i + " "
inputFiles = []
for i in files:
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = os.path.basename(i)
inputFile._attachment = open(i, "r")
inputFiles.append(inputFile)
if cmdline == "":
if self.hasInputFromPort('commandLine'):
cmdline = self.getInputFromPort('commandLine')
if self.hasInputFromPort('numProcs'):
numProcs = self.getInputFromPort('numProcs')
if self.hasInputFromPort("inFiles"):
inFilesPath = self.getInputFromPort("inFiles")
if inFilesPath != None:
for i in inFilesPath:
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = os.path.basename(i)
inputFile._attachment = open(i, "r")
inputFiles.append(inputFile)
print os.path.basename(url) + " from " + os.path.dirname(url) + " is going to run with arguments:\n " + cmdline
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(url)
req = launchJobRequest()
req._argList = cmdline
req._inputFile = inputFiles
if numProcs != None:
req._numProcs = numProcs
resp = appServicePort.launchJob(req)
self.jobID = resp._jobID
print "Job outputs URL: " + resp._status._baseURL # urlparse.urljoin(url, '/' + self.jobID)
status = resp._status._code
while (status != 4 and status != 8):
status = appServicePort.queryStatus(queryStatusRequest(self.jobID))._code
time.sleep(5)
if (status == 8):
resp = appServicePort.getOutputs(getOutputsRequest(self.jobID))
outurls = [str(resp._stdOut), str(resp._stdErr)]
if (resp._outputFile != None):
for i in resp._outputFile:
outurls.append(str(i._url))
print "Opal job completed successfully"
else:
print "ERROR: Opal job failed"
resp = appServicePort.getOutputs(getOutputsRequest(self.jobID))
outurls = [str(resp._stdOut), str(resp._stdErr)]
self.setResult("outurls", tuple(outurls))
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
else:
progress = None
# 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]
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 != "version_mismatch"):
runtime = time.time() - starttime
elif progress == "complete":
endtimefile = open(
'%s%s%s/%s_end_time' %
(INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value))
runtime = float(endtimefile.read()) - starttime
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())
elif progress == "error":
print printheader("%s Job Status Page - Error" % calctype.upper(), 0)
elif progress == "running": # job is not complete, refresh in 30 seconds
print printheader("%s Job Status Page" % calctype.upper(), refresh)
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>"
if calctype == "pdb2pqr":
if have_opal:
# Getting PDB2PQR Opal run log info
if os.path.isfile('%s%s%s/pdb2pqr_opal_log' %
(INSTALLDIR, TMPDIR, form["jobid"].value)):
pdb2pqrOpalLogFile = open(
'%s%s%s/pdb2pqr_opal_log' %
(INSTALLDIR, TMPDIR, form["jobid"].value), 'r')
logstr = pdb2pqrOpalLogFile.read().split('\n')
logopts = eval(logstr[0])
logff = logstr[1]
REMOTE_ADDR = logstr[2]
pdb2pqrOpalLogFile.close()
for i in range(0, len(filelist)):
if filelist[i]._name[-7:] == ".propka" or (
filelist[i]._name[-13:] == "-typemap.html"
and typemap == True
) or filelist[i]._name[-4:] == ".pqr" or filelist[i]._name[
-3:] == ".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)
logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR)
else:
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)
#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))
syscommand = 'zip -9 ' + filelist[
i]._name + '.zip ' + filelist[i]._name
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = filelist[i]._name + '.zip'
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)
syscommand = 'zip -9 ' + os.path.basename(
outputfile) + '.zip ' + os.path.basename(outputfile)
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = outputfile + ".zip"
print "<li><a href=%s%s%s/%s>%s</a></li>" % (
WEBSITE, TMPDIR, jobid,
os.path.basename(outputfilezip),
os.path.basename(outputfilezip))
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><a href=%s>Click here</a> to run APBS with your results.</p>" % nexturl
elif calctype == "apbs":
print "</ul></p><hr><p><a href=%s>Click here</a> to visualize your results.</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\">"
print "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
print "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
print "</script>"
print "<script type=\"text/javascript\">"
print "try {"
print "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
if logopts != {}:
for key in logopts:
print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (
key, logopts[key])
print "pageTracker._trackPageview();"
print "} catch(err) {}</script>"
print "</BODY>"
print "</HTML>"
