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)
class OpalService:
def __init__(self, serviceName=None,
opalURL="http://webservices.rbvi.ucsf.edu/opal/services/",
sessionData=None):
from AppService_client import AppServiceLocator
from AppService_client import getAppMetadataRequest
self.busy = False
self.appLocator = AppServiceLocator()
if sessionData:
self.serviceURL, self.jobID, self.status = sessionData
try:
from cPickle import loads
except ImportError:
from pickle import loads
else:
self.serviceURL = opalURL + serviceName
self.jobID = None
self.status = None
self.appServicePort = self.appLocator.getAppServicePort(
self.serviceURL)
if not sessionData:
req = getAppMetadataRequest()
resp = self.appServicePort.getAppMetadata(req)
#print resp._usage
def sessionData(self):
return self.serviceURL, self.jobID, self.status
def _saveStatus(self, status):
self.status = (status._code, status._message, status._baseURL)
def currentStatus(self):
if self.status:
return self.status[1]
elif self.busy:
return "waiting for response from Opal server"
else:
return "no Opal job running"
def launchJob(self, cmdLine, **kw):
if self.jobID is not None or self.busy:
raise RuntimeError("Job has been launched already")
import chimera
from AppService_client import launchJobRequest
import socket
req = launchJobRequest()
req._argList = cmdLine
for key, value in kw.iteritems():
setattr(req, key, value)
if chimera.nogui:
try:
resp = self.appServicePort.launchJob(req)
except socket.error, e:
from chimera import NonChimeraError
raise NonChimeraError(str(e))
self.jobID = resp._jobID
self._saveStatus(resp._status)
else:
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)
class OpalService:
def __init__(self,
serviceName=None,
opalURL="http://webservices.rbvi.ucsf.edu/opal/services/",
sessionData=None):
from AppService_client import AppServiceLocator
from AppService_client import getAppMetadataRequest
self.busy = False
self.appLocator = AppServiceLocator()
if sessionData:
self.serviceURL, self.jobID, self.status = sessionData
try:
from cPickle import loads
except ImportError:
from pickle import loads
else:
self.serviceURL = opalURL + serviceName
self.jobID = None
self.status = None
self.appServicePort = self.appLocator.getAppServicePort(
self.serviceURL)
if not sessionData:
req = getAppMetadataRequest()
resp = self.appServicePort.getAppMetadata(req)
#print resp._usage
def sessionData(self):
return self.serviceURL, self.jobID, self.status
def _saveStatus(self, status):
self.status = (status._code, status._message, status._baseURL)
def currentStatus(self):
if self.status:
return self.status[1]
elif self.busy:
return "waiting for response from Opal server"
else:
return "no Opal job running"
def launchJob(self, cmdLine, **kw):
if self.jobID is not None or self.busy:
raise RuntimeError("Job has been launched already")
import chimera
from AppService_client import launchJobRequest
import socket
req = launchJobRequest()
req._argList = cmdLine
for key, value in kw.iteritems():
setattr(req, key, value)
if chimera.nogui:
try:
resp = self.appServicePort.launchJob(req)
except socket.error, e:
from chimera import NonChimeraError
raise NonChimeraError(str(e))
self.jobID = resp._jobID
self._saveStatus(resp._status)
else:
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 __init__(self,
serviceName=None,
opalURL="http://webservices.rbvi.ucsf.edu/opal/services/",
sessionData=None):
from AppService_client import AppServiceLocator
from AppService_client import getAppMetadataRequest
self.busy = False
self.appLocator = AppServiceLocator()
if sessionData:
self.serviceURL, self.jobID, self.status = sessionData
try:
from cPickle import loads
except ImportError:
from pickle import loads
else:
self.serviceURL = opalURL + serviceName
self.jobID = None
self.status = None
self.appServicePort = self.appLocator.getAppServicePort(
self.serviceURL)
if not sessionData:
req = getAppMetadataRequest()
resp = self.appServicePort.getAppMetadata(req)
def __init__(self, serviceName=None, opalURL="http://webservices.rbvi.ucsf.edu/opal/services/", sessionData=None): from AppService_client import AppServiceLocator from AppService_client import getAppMetadataRequest self.busy = False self.appLocator = AppServiceLocator() if sessionData: self.serviceURL, self.jobID, self.status = sessionData try: from cPickle import loads except ImportError: from pickle import loads else: self.serviceURL = opalURL + serviceName self.jobID = None self.status = None self.appServicePort = self.appLocator.getAppServicePort( self.serviceURL) if not sessionData: req = getAppMetadataRequest() resp = self.appServicePort.getAppMetadata(req)
def mainCGI():
"""
Main driver for running PDB2PQR from a web page
"""
print "Content-type: text/html\n"
import cgi
import cgitb
cgitb.enable()
form = cgi.FieldStorage()
ff = form["FF"].value
input = 0
apbs_input = form.has_key("INPUT")
typemap = form.has_key("TYPEMAP")
neutraln = form.has_key("NEUTRALN")
neutralc = form.has_key("NEUTRALC")
if HAVE_PDB2PQR_OPAL == "1":
have_opal = True
# Opal-specific import statments
from AppService_client import AppServiceLocator, getAppMetadataRequest, launchJobRequest, launchJobBlockingRequest, getOutputAsBase64ByNameRequest
from AppService_types import ns0
from ZSI.TC import String
else:
have_opal = False
if have_opal:
options = {}
options["ff"] = ff
fffile = None
namesfile = None
else:
options = {"extensions": {}}
if form.has_key("DEBUMP"):
options["debump"] = 1
else:
options["debump"] = 0
if form.has_key("OPT"):
options["opt"] = 1
else:
options["opt"] = 0
if form.has_key("PROPKA"):
try:
ph = float(form["PH"].value)
if ph < 0.0 or ph > 14.0: raise ValueError
options["ph"] = ph
except ValueError:
text = "The entered pH of %.2f is invalid! " % form["PH"].value
text += "Please choose a pH between 0.0 and 14.0."
#print "Content-type: text/html\n"
print text
sys.exit(2)
if form.has_key("PDBID"):
pdbfile = getPDBFile(form["PDBID"].value)
pdbfilename = form["PDBID"].value
elif form.has_key("PDB"):
pdbfile = StringIO(form["PDB"].value)
pdbfilename = form["PDB"].filename
pdbfilename = re.split(r'[/\\]', pdbfilename)[-1]
if form.has_key("INPUT"):
input = 1
options["apbs"] = 1
if form.has_key("USERFF"):
if have_opal:
ffname = form["USERFF"].filename
ffname = re.split(r'[/\\]', ffname)[-1]
if ffname[-4:] == ".DAT":
ffname = ffname[:-4]
fffile = StringIO(form["USERFF"].value)
namesfile = StringIO(form["USERNAMES"].value)
options["ff"] = ffname
options["userff"] = fffile
options["usernames"] = namesfile
else:
userff = StringIO(form["USERFF"].value)
usernames = StringIO(form["USERNAMES"].value)
options["ff"] = "user-defined"
options["userff"] = userff
options["usernames"] = usernames
if form.has_key("FFOUT"):
if form["FFOUT"].value != "internal":
options["ffout"] = form["FFOUT"].value
if form.has_key("CHAIN"):
options["chain"] = 1
if form.has_key("WHITESPACE"):
options["whitespace"] = 1
if form.has_key("TYPEMAP"):
options["typemap"] = 1
if form.has_key("NEUTRALN"):
options["neutraln"] = 1
if form.has_key("NEUTRALC"):
options["neutralc"] = 1
if form.has_key("LIGAND"):
if have_opal:
ligandfilename = str(form["LIGAND"].filename)
ligandfilename = re.split(r'[/\\]', ligandfilename)[-1]
# for Windows-style newline compatibility
templigandfilename = tempfile.mkstemp()[1]
templigandfile = open(templigandfilename, 'w')
templigandfile.write(form["LIGAND"].value)
templigandfile.close()
templigandfile = open(templigandfilename, 'rU')
if have_opal:
options["ligand"] = templigandfile.read()
else:
templigandstring = templigandfile.read(
) # this variable is used again later to write this file to output
options["ligand"] = StringIO(templigandstring)
templigandfile.close()
if not have_opal:
pdbfilestring = pdbfile.read()
pdblist, errlist = readPDB(StringIO(pdbfilestring))
dummydef = Definition()
dummyprot = Protein(pdblist, dummydef)
if len(pdblist) == 0 and len(errlist) == 0:
text = "Unable to find PDB file - Please make sure this is "
text += "a valid PDB file ID!"
#print "Content-type: text/html\n"
print text
sys.exit(2)
elif dummyprot.numAtoms() > MAXATOMS and "opt" in options:
text = "<HTML><HEAD>"
text += "<TITLE>PDB2PQR Error</title>"
text += "<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">" % STYLESHEET
text += "</HEAD><BODY><H2>PDB2PQR Error</H2><P>"
text += "Due to server limits, we are currently unable to optimize "
text += "proteins of greater than MAXATOMS atoms on the server (PDB2PQR "
text += "found %s atoms in the selected PDB file). If you " % dummyprot.numAtoms(
)
text += "want to forgo optimization please try the server again.<P>"
text += "Otherwise you may use the standalone version of PDB2PQR that "
text += "is available from the <a href=\"http://pdb2pqr.sourceforge.net\">"
text += "PDB2PQR SourceForge project page</a>."
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\");"
for key in options:
text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (
key, options[key])
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text += "</BODY></HTML>"
#print "Content-type: text/html\n"
print text
sys.exit(2)
try:
if have_opal:
ligandFile = None
ffFile = None
namesFile = None
#else:
starttime = time.time()
name = setID(starttime)
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),
'w')
apbsInputFile.write(str(apbs_input))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),
'w')
typemapInputFile.write(str(typemap))
typemapInputFile.close()
if have_opal:
myopts = ""
for key in options:
if key == "opt":
if options[key] == 0:
# user does not want optimization
key = "noopt"
else:
# pdb2pqr optimizes by default, don't bother with flag
continue
elif key == "debump":
if options[key] == 0:
# user does not want debumping
key = "nodebump"
else:
# pdb2pqr debumps by default, so change this flag to --nodebump
continue
elif key == "ph":
val = options[key]
key = "with-ph=%s" % val
elif key == "ffout":
val = options[key]
key = "ffout=%s" % val
elif key == "ligand":
val = ligandfilename
key = "ligand=%s" % val
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = val
ligandFile._contents = options["ligand"]
elif key == "apbs":
key = "apbs-input"
elif key == "chain":
key = "chain"
elif key == "whitespace":
key = "whitespace"
elif key == "typemap":
key = "typemap"
elif key == "ff":
val = options[key]
key = "ff=%s" % val
if fffile:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = val + ".DAT"
ffFileString = fffile.read()
ffFile._contents = ffFileString
if namesfile:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = val + ".names"
namesFileString = namesfile.read()
namesFile._contents = namesFileString
if key not in ["userff", "usernames"]:
myopts += "--" + str(key) + " "
myopts += str(pdbfilename) + " "
if pdbfilename[-4:] == ".pdb":
myopts += "%s.pqr" % str(pdbfilename[:-4])
else:
myopts += "%s.pqr" % str(pdbfilename)
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
# launch job
req = launchJobRequest()
req._argList = myopts
inputFiles = []
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = pdbfilename
pdbOpalFile._contents = pdbfile.read()
pdbfile.close()
inputFiles.append(pdbOpalFile)
if ligandFile:
inputFiles.append(ligandFile)
if ffFile:
inputFiles.append(ffFile)
if namesFile:
inputFiles.append(namesFile)
req._inputFile = inputFiles
try:
resp = appServicePort.launchJob(req)
except Exception, e:
printHeader("PDB2PQR Job Submission - Error")
print "<BODY>\n<P>"
print "There was an error with your job submission<br>"
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\");"
for key in options:
print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (
key, options[key])
print "pageTracker._trackPageview();"
print "} catch(err) {}</script>"
print "</BODY>"
print "</HTML>"
sys.exit(2)
#printHeader("PDB2PQR Job Submission",have_opal,jobid=resp._jobID)
pdb2pqrOpalJobIDFile = open(
'%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalJobIDFile.write(resp._jobID)
pdb2pqrOpalJobIDFile.close()
print redirector(name)
if options.has_key("userff"):
options["userff"] = ffFileString
if options.has_key("usernames"):
options["usernames"] = namesFileString
# Recording CGI run information for PDB2PQR Opal
pdb2pqrOpalLogFile = open(
'%s%s%s/pdb2pqr_opal_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalLogFile.write(
str(options) + '\n' + str(ff) + '\n' +
str(os.environ["REMOTE_ADDR"]))
pdb2pqrOpalLogFile.close()
else:
def __init__(self, url):
self.url = url
appLocator = AppServiceLocator()
self.appServicePort = appLocator.getAppServicePort(self.url)
def execApbs(vars=None, argv=None):
""" Executes APBS and regulates checking of job status and retrieval of data if job is successfully completed. """
if argv is None:
# i.e. if it is a local run
argv = sys.argv
webRun = False
else:
webRun = True
custom_service_url = None
if vars != None:
if vars.has_key('service_url'):
custom_service_url = vars['service_url']
vars = initRemoteVars(argv)
if custom_service_url != None:
vars['service_url'] = custom_service_url
global service_url
#*argument parser
# command-line arguments
vars['inFile'] = argv[-1]
# parses input file
if (vars['inFile'].find("/") == -1):
directory = ""
else:
directory = os.path.dirname(vars['inFile']) + '/'
vars['inFile'] = os.path.basename(vars['inFile'])
nprocs = 1
if not vars.has_key('service_url'):
# find out if it's sequential or parallel
tempFile = open(directory + vars['inFile'], 'r')
version_check_flag = True
for line in tempFile:
# remove whitespace
line = line.strip()
if (line[:5] == 'pdime'):
dimension_array = line.split()
nprocs = int(dimension_array[1]) * int(
dimension_array[2]) * int(dimension_array[3])
global parallel_service_url
vars['service_url'] = parallel_service_url
version_check_flag = False
if (line[:5] == 'async'):
vars['service_url'] = service_url
version_check_flag = True
break
if version_check_flag:
vars['service_url'] = service_url
tempFile.close()
else:
version_check_flag = True # Enable version checking for custom defined Opal service as well
service_url = vars['service_url']
# Retrieve a reference to the AppServicePort
#*this is also from the path to the service
appServicePort = AppServiceLocator().getAppServicePort(vars['service_url'])
# Set up remote job launch
req = launchJobRequest()
# Checks version compatibility (but currently only works for sequential calculations)
if version_check_flag:
opal_version = AppServicePortTypeSoapBindingSOAP(
vars['service_url']).getAppMetadata(
getAppMetadataRequest())._usage.split()[-1]
if opal_version != local_version:
stderr.write(
"WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n"
)
stderr.write(
"It appears that the remote server version of APBS (%s) does not match\nthe local version (%s)!\n"
% (opal_version, local_version))
stderr.write("Proceed at your own risk!!\n")
stderr.write(
"WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n"
)
if webRun:
return False
if (vars.has_key('argList')):
vars['argList'] = vars['argList'] + " " + vars['inFile']
else:
vars['argList'] = vars['inFile']
req._argList = vars['argList']
req._numProcs = nprocs
# append all input files in this manner - in this case we have two of them
inputFiles = []
#*this is where apbs.in is read in
inputFiles.append(ns0.InputFileType_Def('inputFile'))
#*this must be the same as req._argList is defined to be
inputFiles[-1]._name = vars['inFile']
tempFile = open(directory + vars['inFile'], 'r')
inputFiles[-1]._contents = tempFile.read()
tempFile.close()
# this is where the rest of the files to read in are determined
start = False
tempFile = open(directory + vars['inFile'], 'r')
for line in tempFile:
# remove whitespace
line = line.strip()
if (line == "end"):
break
if (start and line.find("#") != 0):
# eliminates lines with just comments
# remove comment
if (line.find("#") != -1):
line = line[:line.find("#")]
# re-remove whitespace (left after comment removal)
line = line.strip()
# remove everything except file name
count = -1
while line[count] != ' ':
count = count - 1
fileName = line[count + 1:]
inputFiles.append(ns0.InputFileType_Def('inputFile'))
inputFiles[-1]._name = fileName
tempFile2 = open(directory + fileName, "r")
inputFiles[-1]._contents = tempFile2.read()
tempFile2.close()
if (line == "read"):
start = True
tempFile.close()
# req's inputFile variable is the array of input files created in the lines directly above
req._inputFile = inputFiles
if vars['typeOfRun'] == 'remote':
appServicePort.launchJob(req)
return [appServicePort, appServicePort.launchJob(req)]
# Launch job, and retrieve job ID
print "Launching remote APBS job"
try:
resp = appServicePort.launchJob(req)
except ZSI.FaultException, errstr:
stderr.write(
"Error! Failed to execute Opal job. Please send the entire output to the APBS development team.\n"
)
stderr.write("%s\n" % errstr.fault.AsSoap())
sys.exit(13)
# Import the Opal libraries
from AppService_client import \
AppServiceLocator, getAppMetadataRequest, launchJobRequest, \
queryStatusRequest, getOutputsRequest, \
launchJobBlockingRequest, getOutputAsBase64ByNameRequest
from AppService_types import ns0
from os import mkdir
from time import sleep
from ZSI.TC import String
# Set the location of our service
# A list of NBCR services can be found at http://ws.nbcr.net/opal2/dashboard?command=serviceList
serviceURL = "http://ws.nbcr.net/opal2/services/MEME_4.4.0"
# Instantiate a new service object to interact with. Pass it the service location
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(serviceURL)
# Instantiate a new non-blocking job request
req = launchJobRequest()
# Set the command-line arguments for the job.
# Use DNA alphabet, and find 3 motifs.
req._argList = "meme crp0.fasta -dna -mod zoops -nmotifs 3"
# Get contents of local file to be used as input
fastaFile = open("./crp0.fasta", "r")
fastaFileContents = fastaFile.read()
fastaFile.close()
# Set name and content of remote input file.
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 handleOpal(weboptions):
'''
Handle opal based run.
'''
# Opal-specific import statements
from AppService_client import AppServiceLocator, launchJobRequest
from AppService_types import ns0
inputFiles = []
if 'userff' in weboptions:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = weboptions.userfffilename
ffFile._contents = weboptions.userffstring
inputFiles.append(ffFile)
if 'usernames' in weboptions:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = weboptions.usernamesfilename
namesFile._contents = weboptions.usernamesstring
inputFiles.append(namesFile)
if 'ligand' in weboptions:
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = weboptions.ligandfilename
ligandFile._contents = weboptions.ligandfilestring
inputFiles.append(ligandFile)
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = weboptions.pdbfilename
pdbOpalFile._contents = weboptions.pdbfilestring
inputFiles.append(pdbOpalFile)
# launch job
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
req = launchJobRequest()
req._argList = weboptions.getCommandLine()
req._inputFile = inputFiles
try:
resp = appServicePort.launchJob(req)
except Exception, e:
printHeader("PDB2PQR Job Submission - Error")
print "<BODY>\n<P>"
print "There was an error with your job submission<br>"
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\");"
for key in weboptions:
print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (
key, weboptions[key])
print "pageTracker._trackPageview();"
print "} catch(err) {}</script>"
print "</BODY>"
print "</HTML>"
sys.exit(2)
def handleOpal(weboptions):
'''
Handle opal based run.
'''
# Opal-specific import statements
from AppService_client import AppServiceLocator, launchJobRequest
from AppService_types import ns0
inputFiles = []
if 'userff' in weboptions:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = weboptions.userfffilename
ffFile._contents = weboptions.userffstring
inputFiles.append(ffFile)
if 'usernames' in weboptions:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = weboptions.usernamesfilename
namesFile._contents = weboptions.usernamesstring
inputFiles.append(namesFile)
if 'ligand' in weboptions:
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = weboptions.ligandfilename
ligandFile._contents = weboptions.ligandfilestring
inputFiles.append(ligandFile)
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = weboptions.pdbfilename
pdbOpalFile._contents = weboptions.pdbfilestring
inputFiles.append(pdbOpalFile)
# launch job
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
req = launchJobRequest()
req._argList = weboptions.getCommandLine()
req._inputFile=inputFiles
try:
resp=appServicePort.launchJob(req)
except Exception as e:
printHeader("PDB2PQR Job Submission - Error")
print("<BODY>\n<P>")
print("There was an error with your job submission<br>")
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\");")
for key in weboptions:
print("pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key]))
print("pageTracker._trackPageview();")
print("} catch(err) {}</script>")
print("</BODY>")
print("</HTML>")
sys.exit(2)
try:
starttime = time.time()
name = setID(starttime)
#Some job parameters logging.
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),'w')
apbsInputFile.write(str(weboptions["apbs"]))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),'w')
typemapInputFile.write(str(weboptions["typemap"]))
typemapInputFile.close()
pdb2pqrOpalJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalJobIDFile.write(resp._jobID)
pdb2pqrOpalJobIDFile.close()
print(redirector(name, weboptions))
# Recording CGI run information for PDB2PQR Opal
pdb2pqrOpalLogFile = open('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalLogFile.write(str(weboptions.getOptions())+'\n'+
str(os.environ["REMOTE_ADDR"]))
pdb2pqrOpalLogFile.close()
except Exception as details:
print(details)
createError(name, details)
def execApbs(vars=None, argv=None):
""" Executes APBS and regulates checking of job status and retrieval of data if job is successfully completed. """
if argv is None:
# i.e. if it is a local run
argv = sys.argv
webRun = False
else:
webRun = True
custom_service_url = None
if vars != None:
if vars.has_key('service_url'):
custom_service_url = vars['service_url']
vars = initRemoteVars(argv)
if custom_service_url != None:
vars['service_url'] = custom_service_url
global service_url
#*argument parser
# command-line arguments
vars['inFile'] = argv[-1]
# parses input file
if(vars['inFile'].find("/")==-1):
directory=""
else:
directory = os.path.dirname(vars['inFile'])+'/'
vars['inFile'] = os.path.basename(vars['inFile'])
nprocs = 1
if not vars.has_key('service_url'):
# find out if it's sequential or parallel
tempFile = open(directory+vars['inFile'], 'r')
version_check_flag = True
for line in tempFile:
# remove whitespace
line=line.strip()
if(line[:5]=='pdime'):
dimension_array = line.split()
nprocs = int(dimension_array[1])*int(dimension_array[2])*int(dimension_array[3])
global parallel_service_url
vars['service_url'] = parallel_service_url
version_check_flag = False
if(line[:5]=='async'):
vars['service_url'] = service_url
version_check_flag = True
break
if version_check_flag:
vars['service_url'] = service_url
tempFile.close()
else:
version_check_flag = True # Enable version checking for custom defined Opal service as well
service_url = vars['service_url']
# Retrieve a reference to the AppServicePort
#*this is also from the path to the service
appServicePort = AppServiceLocator().getAppServicePort(vars['service_url'])
# Set up remote job launch
req = launchJobRequest()
# Checks version compatibility (but currently only works for sequential calculations)
if version_check_flag:
opal_version = AppServicePortTypeSoapBindingSOAP(vars['service_url']).getAppMetadata(getAppMetadataRequest())._usage.split()[-1]
if opal_version != local_version:
stderr.write("WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n")
stderr.write("It appears that the remote server version of APBS (%s) does not match\nthe local version (%s)!\n" % (opal_version,local_version))
stderr.write("Proceed at your own risk!!\n")
stderr.write("WARNING! WARNING! WARNING! WARNING! WARNING! WARNING! WARNING!\n")
if webRun:
return False
if(vars.has_key('argList')):
vars['argList'] = vars['argList'] + " " + vars['inFile']
else:
vars['argList']=vars['inFile']
req._argList = vars['argList']
req._numProcs = nprocs
# append all input files in this manner - in this case we have two of them
inputFiles = []
#*this is where apbs.in is read in
inputFiles.append(ns0.InputFileType_Def('inputFile'))
#*this must be the same as req._argList is defined to be
inputFiles[-1]._name = vars['inFile']
tempFile = open(directory+vars['inFile'], 'r')
inputFiles[-1]._contents = tempFile.read()
tempFile.close()
# this is where the rest of the files to read in are determined
start = False
tempFile = open(directory+vars['inFile'], 'r')
for line in tempFile:
# remove whitespace
line=line.strip()
if(line=="end"):
break
if(start and line.find("#")!=0):
# eliminates lines with just comments
# remove comment
if(line.find("#")!=-1):
line = line[:line.find("#")]
# re-remove whitespace (left after comment removal)
line=line.strip()
# remove everything except file name
count = -1
while line[count]!=' ':
count = count-1
fileName=line[count+1:]
inputFiles.append(ns0.InputFileType_Def('inputFile'))
inputFiles[-1]._name=fileName
tempFile2 = open(directory+fileName, "r")
inputFiles[-1]._contents = tempFile2.read()
tempFile2.close()
if(line=="read"):
start = True
tempFile.close()
# req's inputFile variable is the array of input files created in the lines directly above
req._inputFile = inputFiles
if vars['typeOfRun']=='remote':
appServicePort.launchJob(req)
return [appServicePort, appServicePort.launchJob(req)]
# Launch job, and retrieve job ID
print "Launching remote APBS job"
try:
resp = appServicePort.launchJob(req)
except ZSI.FaultException, errstr:
stderr.write("Error! Failed to execute Opal job. Please send the entire output to the APBS development team.\n")
stderr.write("%s\n" % errstr.fault.AsSoap())
sys.exit(13)
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>"
def __init__(self, url):
""" A OpalService can be contructed passing a string containing a valid Opal URL """
self.url = url
appLocator = AppServiceLocator()
self.appServicePort = appLocator.getAppServicePort(self.url)
# set the locations for the X509 certificate and key
#cert = "/Users/sriramkrishnan/certs/apbs_service.cert.pem"
#key = "/Users/sriramkrishnan/certs/apbs_service.privkey"
# If you are using a proxy cert, set both the cert
# and key to the location of the proxy
# Proxies have to be RFC 3820 compliant (use grid-proxy-init -rfc)
cert = "/tmp/x509up_u1000"
key = "/tmp/x509up_u1000"
# Host and port for remote services
baseURL = proto + "://rocks-171.sdsc.edu:8443/"
#baseURL = proto + "://localhost:8080/"
# Retrieve a reference to the AppServicePort
appLocator = AppServiceLocator()
if proto == "http":
appServicePort = appLocator.getAppServicePort(baseURL + "opal2/services/BabelServicePort")
else:
if proto == "https":
# example of ssl invocation
appServicePort = appLocator.getAppServicePort(
baseURL + "opal2/services/cat",
ssl=1,
transdict={'cert_file': cert, 'key_file': key},
transport=httplib.HTTPSConnection)
print "setting cert to: " + cert
else:
print "Unknown protocol: ", proto
sys.exit(1)
def handleOpal(weboptions):
'''
Handle opal based run.
'''
# Opal-specific import statements
from AppService_client import AppServiceLocator, getAppMetadataRequest, launchJobRequest, launchJobBlockingRequest, getOutputAsBase64ByNameRequest
from AppService_types import ns0
inputFiles = []
if 'userff' in weboptions:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = weboptions.userfffilename
ffFile._contents = weboptions.userffstring
inputFiles.append(ffFile)
if 'usernames' in weboptions:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = weboptions.usernamesfilename
namesFile._contents = weboptions.usernamesstring
inputFiles.append(namesFile)
if 'ligand' in weboptions:
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = weboptions.ligandfilename
ligandFile._contents = weboptions.ligandfilestring
inputFiles.append(ligandFile)
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = weboptions.pdbfilename
pdbOpalFile._contents = weboptions.pdbfilestring
inputFiles.append(pdbOpalFile)
# launch job
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
req = launchJobRequest()
req._argList = weboptions.getCommandLine()
req._inputFile=inputFiles
try:
resp=appServicePort.launchJob(req)
except Exception, e:
printHeader("PDB2PQR Job Submission - Error")
print "<BODY>\n<P>"
print "There was an error with your job submission<br>"
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\");"
for key in weboptions:
print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key])
print "pageTracker._trackPageview();"
print "} catch(err) {}</script>"
print "</BODY>"
print "</HTML>"
sys.exit(2)
def mainCGI():
"""
Main driver for running PDB2PQR from a web page
"""
global ligandFile, pdbfilestring, templigandstring, ffFileString, name, pdblist, namesFileString, launchJobRequest, AppServiceLocator, pdbfilename, namesfile, fffile, ns0, ligandfilename, pdbfile, namesFile, ffFile
print("Content-type: text/html\n")
import cgi
import cgitb
cgitb.enable()
form = cgi.FieldStorage()
ff = form["FF"].value
input = 0
apbs_input = "INPUT" in form
typemap = "TYPEMAP" in form
neutraln = "NEUTRALN" in form
neutralc = "NEUTRALC" in form
if HAVE_PDB2PQR_OPAL == "1":
have_opal = True
# Opal-specific import statments
from AppService_client import AppServiceLocator, launchJobRequest
from AppService_types import ns0
from ZSI.TC import String
else:
have_opal = False
if have_opal:
options = {"ff": ff}
fffile = None
namesfile = None
else:
options = {"extensions": {}}
if "DEBUMP" in form:
options["debump"] = 1
else:
options["debump"] = 0
if "OPT" in form:
options["opt"] = 1
else:
options["opt"] = 0
if "PROPKA" in form:
try:
ph = float(form["PH"].value)
if ph < 0.0 or ph > 14.0: raise ValueError
options["ph"] = ph
except ValueError:
text = "The entered pH of %.2f is invalid! " % form["PH"].value
text += "Please choose a pH between 0.0 and 14.0."
# print "Content-type: text/html\n"
print(text)
sys.exit(2)
if "PDBID" in form:
pdbfile = getPDBFile(form["PDBID"].value)
pdbfilename = form["PDBID"].value
elif "PDB" in form:
pdbfile = StringIO(form["PDB"].value)
pdbfilename = form["PDB"].filename
pdbfilename = pdbfilename.split(r'[/\\]')[-1]
if "INPUT" in form:
input = 1
options["apbs"] = 1
if "USERFF" in form:
if have_opal:
ffname = form["USERFF"].filename
ffname = ffname.split(r'[/\\]')[-1]
if ffname[-4:] == ".DAT":
ffname = ffname[:-4]
fffile = StringIO(form["USERFF"].value)
namesfile = StringIO(form["USERNAMES"].value)
options["ff"] = ffname
options["userff"] = fffile
options["usernames"] = namesfile
else:
userff = StringIO(form["USERFF"].value)
usernames = StringIO(form["USERNAMES"].value)
options["ff"] = "user-defined"
options["userff"] = userff
options["usernames"] = usernames
if "FFOUT" in form:
if form["FFOUT"].value != "internal":
options["ffout"] = form["FFOUT"].value
if "CHAIN" in form:
options["chain"] = 1
if "WHITESPACE" in form:
options["whitespace"] = 1
if "TYPEMAP" in form:
options["typemap"] = 1
if "NEUTRALN" in form:
options["neutraln"] = 1
if "NEUTRALC" in form:
options["neutralc"] = 1
if "LIGAND" in form:
if have_opal:
ligandfilename = str(form["LIGAND"].filename)
ligandfilename = ligandfilename.split(r'[/\\]')[-1]
# for Windows-style newline compatibility
templigandfilename = tempfile.mkstemp()[1]
templigandfile = open(templigandfilename, 'w')
templigandfile.write(form["LIGAND"].value)
templigandfile.close()
templigandfile = open(templigandfilename, 'rU')
if have_opal:
options["ligand"] = templigandfile.read()
else:
templigandstring = templigandfile.read() # this variable is used again later to write this file to output
options["ligand"] = StringIO(templigandstring)
templigandfile.close()
if not have_opal:
pdbfilestring = pdbfile.read()
pdblist, errlist = readPDB(StringIO(pdbfilestring))
dummydef = Definition()
dummyprot = Protein(pdblist, dummydef)
if len(pdblist) == 0 and len(errlist) == 0:
text = "Unable to find PDB file - Please make sure this is "
text += "a valid PDB file ID!"
# print "Content-type: text/html\n"
print(text)
sys.exit(2)
elif dummyprot.numAtoms() > MAXATOMS and "opt" in options:
text = "<HTML><HEAD>"
text += "<TITLE>PDB2PQR Error</title>"
text += "<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">" % STYLESHEET
text += "</HEAD><BODY><H2>PDB2PQR Error</H2><P>"
text += "Due to server limits, we are currently unable to optimize "
text += "proteins of greater than MAXATOMS atoms on the server (PDB2PQR "
text += "found %s atoms in the selected PDB file). If you " % dummyprot.numAtoms()
text += "want to forgo optimization please try the server again.<P>"
text += "Otherwise you may use the standalone version of PDB2PQR that "
text += "is available from the <a href=\"http://pdb2pqr.sourceforge.net\">"
text += "PDB2PQR SourceForge project page</a>."
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\");"
for key in options:
text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, options[key])
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text += "</BODY></HTML>"
# print "Content-type: text/html\n"
print(text)
sys.exit(2)
try:
if have_opal:
ligandFile = None
ffFile = None
namesFile = None
# else:
starttime = time.time()
name = setID(starttime)
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name), 'w')
apbsInputFile.write(str(apbs_input))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name), 'w')
typemapInputFile.write(str(typemap))
typemapInputFile.close()
if have_opal:
myopts = ""
for key in options:
if key == "opt":
if options[key] == 0:
# user does not want optimization
key = "noopt"
else:
# pdb2pqr optimizes by default, don't bother with flag
continue
elif key == "debump":
if options[key] == 0:
# user does not want debumping
key = "nodebump"
else:
# pdb2pqr debumps by default, so change this flag to --nodebump
continue
elif key == "ph":
val = options[key]
key = "with-ph=%s" % val
elif key == "ffout":
val = options[key]
key = "ffout=%s" % val
elif key == "ligand":
val = ligandfilename
key = "ligand=%s" % val
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = val
ligandFile._contents = options["ligand"]
elif key == "apbs":
key = "apbs-input"
elif key == "chain":
key = "chain"
elif key == "whitespace":
key = "whitespace"
elif key == "typemap":
key = "typemap"
elif key == "ff":
val = options[key]
key = "ff=%s" % val
if fffile:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = val + ".DAT"
ffFileString = fffile.read()
ffFile._contents = ffFileString
if namesfile:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = val + ".names"
namesFileString = namesfile.read()
namesFile._contents = namesFileString
if key not in ["userff", "usernames"]:
myopts += "--" + str(key) + " "
myopts += str(pdbfilename) + " "
if pdbfilename[-4:] == ".pdb":
myopts += "%s.pqr" % str(pdbfilename[:-4])
else:
myopts += "%s.pqr" % str(pdbfilename)
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
# launch job
req = launchJobRequest()
req._argList = myopts
inputFiles = []
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = pdbfilename
pdbOpalFile._contents = pdbfile.read()
pdbfile.close()
inputFiles.append(pdbOpalFile)
if ligandFile:
inputFiles.append(ligandFile)
if ffFile:
inputFiles.append(ffFile)
if namesFile:
inputFiles.append(namesFile)
req._inputFile = inputFiles
try:
resp = appServicePort.launchJob(req)
except Exception as e:
printHeader("PDB2PQR Job Submission - Error")
print("<BODY>\n<P>")
print("There was an error with your job submission<br>")
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\");")
for key in options:
print("pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, options[key]))
print("pageTracker._trackPageview();")
print("} catch(err) {}</script>")
print("</BODY>")
print("</HTML>")
sys.exit(2)
# printHeader("PDB2PQR Job Submission",have_opal,jobid=resp._jobID)
pdb2pqrOpalJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalJobIDFile.write(resp._jobID)
pdb2pqrOpalJobIDFile.close()
print(redirector(name))
if "userff" in options:
options["userff"] = ffFileString
if "usernames" in options:
options["usernames"] = namesFileString
# Recording CGI run information for PDB2PQR Opal
pdb2pqrOpalLogFile = open('%s%s%s/pdb2pqr_opal_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalLogFile.write(str(options) + '\n' + str(ff) + '\n' + str(os.environ["REMOTE_ADDR"]))
pdb2pqrOpalLogFile.close()
else:
# pqrpath = startServer(name)
statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
statusfile.write('running')
statusfile.close()
pid = os.fork()
if pid:
print(redirector(name))
sys.exit()
else:
currentdir = os.getcwd()
os.chdir("/")
os.setsid()
os.umask(0)
os.chdir(currentdir)
os.close(1) # not sure if these
os.close(2) # two lines are necessary
pqrpath = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, name, name)
options["outname"] = pqrpath
options["verbose"] = ""
orig_stdout = sys.stdout
orig_stderr = sys.stderr
sys.stdout = open('%s%s%s/pdb2pqr_stdout.txt' % (INSTALLDIR, TMPDIR, name), 'w')
sys.stderr = open('%s%s%s/pdb2pqr_stderr.txt' % (INSTALLDIR, TMPDIR, name), 'w')
header, lines, missedligands = runPDB2PQR(pdblist, ff, options)
sys.stdout.close()
sys.stderr.close()
sys.stdout = orig_stdout
sys.stderr = orig_stderr
endtimefile = open('%s%s%s/pdb2pqr_end_time' % (INSTALLDIR, TMPDIR, name), 'w')
endtimefile.write(str(time.time()))
endtimefile.close()
pqrfile = open(pqrpath, "w")
pqrfile.write(header)
for line in lines: # type: object
# Adding whitespaces if --whitespace is in the options
if "whitespace" in options.keys() and options["whitespace"] == 1:
if line[0:4] == 'ATOM':
newline = line[0:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % newline.strip())
elif line[0:6] == 'HETATM':
newline = line[0:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
pqrfile.write("%s\n" % newline.strip())
else:
pqrfile.write("%s\n" % line.strip())
pqrfile.close()
if input:
from src import inputgen as Inp
from src import psize as Pz
method = "mg-auto"
size = Pz.Psize()
size.parseInput(pqrpath)
size.runPsize(pqrpath)
async = 0 # No async files here!
myinput = Inp.Input(pqrpath, size, method, async)
myinput.printInputFiles()
myinput.dumpPickle()
endtime = time.time() - starttime
# createResults(header, input, name, endtime, missedligands)
logRun(options, endtime, len(lines), ff, os.environ["REMOTE_ADDR"])
# printHeader("PDB2PQR Job Submission",have_opal,jobid=name)
if "LIGAND" in form:
outputligandfile = open('%s%s%s/%s.mol2' % (INSTALLDIR, TMPDIR, name, name), 'w')
outputligandfile.write(templigandstring)
outputligandfile.close()
outputpdbfile = open('%s%s%s/%s.pdb' % (INSTALLDIR, TMPDIR, name, name), 'w')
outputpdbfile.write(pdbfilestring)
outputpdbfile.close()
statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
statusfile.write('complete\n')
filelist = glob.glob('%s%s%s/%s*' % (INSTALLDIR, TMPDIR, name, name))
for filename in filelist:
statusfile.write(filename + '\n')
statusfile.close()
except SystemError.StandardError as details:
print(details)
createError(name, details)
def mainCGI():
"""
Opal driver for running PDB2PQR from a web page
"""
serviceURL = OPALURL
cgitb.enable()
form = cgi.FieldStorage()
options = {}
ff = form["FF"].value
options["ff"] = ff
fffile = None
input = 0
if form.has_key("DEBUMP"): options["debump"] = 1
else: options["debump"] = 0
if form.has_key("OPT"): options["opt"] = 1
else: options["opt"] = 0
if form.has_key("PROPKA"):
try:
ph = float(form["PH"].value)
if ph < 0.0 or ph > 14.0: raise ValueError
options["ph"] = ph
except ValueError:
text = "The entered pH of %.2f is invalid! " % form["PH"].value
text += "Please choose a pH between 0.0 and 14.0."
# print "Content-type: text/html\n"
print text
sys.exit(2)
if form.has_key("PDBID"):
filename = form["PDBID"].value
infile = getPDBFile(form["PDBID"].value)
elif form.has_key("PDB"):
filename = form["PDB"].filename
filename=re.split(r'[/\\]',filename)[-1]
infile = StringIO(form["PDB"].value)
if form.has_key("INPUT"):
input = 1
options["apbs"] = 1
if form.has_key("USERFF"):
# userff = StringIO(form["USERFF"].value)
# ff = "user-defined"
# options["userff"] = userff
ffname = form["USERFF"].filename
ffname = re.split(r'[/\\]',ffname)[-1]
fffile = StringIO(form["USERFF"].value)
options["ff"] = ffname
if form.has_key("FFOUT"):
if form["FFOUT"].value != "internal":
options["ffout"] = form["FFOUT"].value
if form.has_key("CHAIN"):
options["chain"] = 1
if form.has_key("WHITESPACE"):
options["whitespace"] = 1
if form.has_key("LIGAND"):
ligandfilename=str(form["LIGAND"].filename)
ligandfilename=re.split(r'[/\\]',ligandfilename)[-1]
options["ligand"] = StringIO(form["LIGAND"].value)
try:
# starttime = time.time()
# name = setID(starttime)
name = filename
ligandFile=None
ffFile=None
# begin SOAP changes
# need to switch options from a dictionary to something resembling a command line query
# such as --chain
myopts=""
for key in options:
if key=="opt":
if options[key]==0:
# user does not want optimization
key="noopt"
else:
# pdb2pqr optimizes by default, don't bother with flag
continue
elif key=="debump":
if options[key]==0:
# user does not want debumping
key="nodebump"
else:
# pdb2pqr debumps by default, so change this flag to --nodebump
continue
elif key=="ph":
val=options[key]
key="with-ph=%s" % val
elif key=="ffout":
val=options[key]
key="ffout=%s" % val
elif key=="ligand":
val=ligandfilename
key="ligand=%s" % val
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = val
ligandFileTemp = open(options["ligand"], "r")
ligandFileString = ligandFileTemp.read()
ligandFileTemp.close()
ligandFile._contents = ligandFileString
elif key=="apbs":
key="apbs-input"
elif key=="chain":
key="chain"
elif key=="whitespace":
key="whitespace"
elif key=="ff":
val=options[key]
key="ff=%s" % val
if fffile:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = val
ffFileTemp = open(fffile, "r")
ffFileString = ffFileTemp.read()
ffFileTemp.close()
ffFile._contents = ffFileString
myopts+="--"+str(key)+" "
myopts+=str(filename)+" "
myopts+="%s.pqr" % str(name)
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(serviceURL)
# launch job
req = launchJobRequest()
req._argList = myopts
inputFiles = []
pdbFile = ns0.InputFileType_Def('inputFile')
pdbFile._name = filename
pdbFile._contents = infile.read()
infile.close()
inputFiles.append(pdbFile)
if ligandFile:
inputFiles.append(ligandFile)
if ffFile:
inputFiles.append(ffFile)
req._inputFile=inputFiles
try:
resp=appServicePort.launchJob(req)
except Exception, e:
printheader("PDB2PQR Job Submission - Error")
print "<BODY>\n<P>"
print "There was an error with your job submission<br>"
print "</P>\n</BODY>"
print "</HTML>"
sys.exit(2)
printheader("PDB2PQR Job Submission",resp._jobID)
def mainCGI():
"""
Main driver for running PDB2PQR from a web page
"""
print "Content-type: text/html\n"
import cgi
import cgitb
cgitb.enable()
form = cgi.FieldStorage()
ff = form["FF"].value
input = 0
apbs_input = form.has_key("INPUT")
typemap = form.has_key("TYPEMAP")
neutraln = form.has_key("NEUTRALN")
neutralc = form.has_key("NEUTRALC")
if HAVE_PDB2PQR_OPAL=="1":
have_opal = True
# Opal-specific import statments
from AppService_client import AppServiceLocator, getAppMetadataRequest, launchJobRequest, launchJobBlockingRequest, getOutputAsBase64ByNameRequest
from AppService_types import ns0
from ZSI.TC import String
else:
have_opal = False
if have_opal:
options = {}
options["ff"] = ff
fffile = None
namesfile = None
else:
options = {"extensions":{}}
if form.has_key("DEBUMP"):
options["debump"] = 1
else:
options["debump"] = 0
if form.has_key("OPT"):
options["opt"] = 1
else:
options["opt"] = 0
if form.has_key("PROPKA"):
try:
ph = float(form["PH"].value)
if ph < 0.0 or ph > 14.0: raise ValueError
options["ph"] = ph
except ValueError:
text = "The entered pH of %.2f is invalid! " % form["PH"].value
text += "Please choose a pH between 0.0 and 14.0."
#print "Content-type: text/html\n"
print text
sys.exit(2)
if form.has_key("PDBID"):
pdbfile = getPDBFile(form["PDBID"].value)
pdbfilename = form["PDBID"].value
elif form.has_key("PDB"):
pdbfile = StringIO(form["PDB"].value)
pdbfilename = form["PDB"].filename
pdbfilename = re.split(r'[/\\]',pdbfilename)[-1]
if form.has_key("INPUT"):
input = 1
options["apbs"] = 1
if form.has_key("USERFF"):
if have_opal:
ffname = form["USERFF"].filename
ffname = re.split(r'[/\\]',ffname)[-1]
if ffname[-4:] == ".DAT":
ffname = ffname[:-4]
fffile = StringIO(form["USERFF"].value)
namesfile = StringIO(form["USERNAMES"].value)
options["ff"] = ffname
options["userff"] = fffile
options["usernames"] = namesfile
else:
userff = StringIO(form["USERFF"].value)
usernames = StringIO(form["USERNAMES"].value)
options["ff"] = "user-defined"
options["userff"] = userff
options["usernames"] = usernames
if form.has_key("FFOUT"):
if form["FFOUT"].value != "internal":
options["ffout"] = form["FFOUT"].value
if form.has_key("CHAIN"):
options["chain"] = 1
if form.has_key("WHITESPACE"):
options["whitespace"] = 1
if form.has_key("TYPEMAP"):
options["typemap"] = 1
if form.has_key("NEUTRALN"):
options["neutraln"] = 1
if form.has_key("NEUTRALC"):
options["neutralc"] = 1
if form.has_key("LIGAND"):
if have_opal:
ligandfilename=str(form["LIGAND"].filename)
ligandfilename=re.split(r'[/\\]',ligandfilename)[-1]
# for Windows-style newline compatibility
templigandfilename = tempfile.mkstemp()[1]
templigandfile = open(templigandfilename,'w')
templigandfile.write(form["LIGAND"].value)
templigandfile.close()
templigandfile = open(templigandfilename,'rU')
if have_opal:
options["ligand"] = templigandfile.read()
else:
templigandstring = templigandfile.read() # this variable is used again later to write this file to output
options["ligand"] = StringIO(templigandstring)
templigandfile.close()
if not have_opal:
pdbfilestring = pdbfile.read()
pdblist, errlist = readPDB(StringIO(pdbfilestring))
dummydef = Definition()
dummyprot = Protein(pdblist, dummydef)
if len(pdblist) == 0 and len(errlist) == 0:
text = "Unable to find PDB file - Please make sure this is "
text += "a valid PDB file ID!"
#print "Content-type: text/html\n"
print text
sys.exit(2)
elif dummyprot.numAtoms() > MAXATOMS and "opt" in options:
text = "<HTML><HEAD>"
text += "<TITLE>PDB2PQR Error</title>"
text += "<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">" % STYLESHEET
text += "</HEAD><BODY><H2>PDB2PQR Error</H2><P>"
text += "Due to server limits, we are currently unable to optimize "
text += "proteins of greater than MAXATOMS atoms on the server (PDB2PQR "
text += "found %s atoms in the selected PDB file). If you " % dummyprot.numAtoms()
text += "want to forgo optimization please try the server again.<P>"
text += "Otherwise you may use the standalone version of PDB2PQR that "
text += "is available from the <a href=\"http://pdb2pqr.sourceforge.net\">"
text += "PDB2PQR SourceForge project page</a>."
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\");"
for key in options:
text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, options[key])
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text += "</BODY></HTML>"
#print "Content-type: text/html\n"
print text
sys.exit(2)
try:
if have_opal:
ligandFile=None
ffFile=None
namesFile=None
#else:
starttime = time.time()
name = setID(starttime)
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),'w')
apbsInputFile.write(str(apbs_input))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),'w')
typemapInputFile.write(str(typemap))
typemapInputFile.close()
if have_opal:
myopts=""
for key in options:
if key=="opt":
if options[key]==0:
# user does not want optimization
key="noopt"
else:
# pdb2pqr optimizes by default, don't bother with flag
continue
elif key=="debump":
if options[key]==0:
# user does not want debumping
key="nodebump"
else:
# pdb2pqr debumps by default, so change this flag to --nodebump
continue
elif key=="ph":
val=options[key]
key="with-ph=%s" % val
elif key=="ffout":
val=options[key]
key="ffout=%s" % val
elif key=="ligand":
val=ligandfilename
key="ligand=%s" % val
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = val
ligandFile._contents = options["ligand"]
elif key=="apbs":
key="apbs-input"
elif key=="chain":
key="chain"
elif key=="whitespace":
key="whitespace"
elif key=="typemap":
key="typemap"
elif key=="ff":
val=options[key]
key="ff=%s" % val
if fffile:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = val + ".DAT"
ffFileString = fffile.read()
ffFile._contents = ffFileString
if namesfile:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = val + ".names"
namesFileString = namesfile.read()
namesFile._contents = namesFileString
if key not in ["userff", "usernames"]:
myopts+="--"+str(key)+" "
myopts+=str(pdbfilename)+" "
if pdbfilename[-4:]==".pdb":
myopts+="%s.pqr" % str(pdbfilename[:-4])
else:
myopts+="%s.pqr" % str(pdbfilename)
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
# launch job
req = launchJobRequest()
req._argList = myopts
inputFiles = []
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = pdbfilename
pdbOpalFile._contents = pdbfile.read()
pdbfile.close()
inputFiles.append(pdbOpalFile)
if ligandFile:
inputFiles.append(ligandFile)
if ffFile:
inputFiles.append(ffFile)
if namesFile:
inputFiles.append(namesFile)
req._inputFile=inputFiles
try:
resp=appServicePort.launchJob(req)
except Exception, e:
printHeader("PDB2PQR Job Submission - Error")
print "<BODY>\n<P>"
print "There was an error with your job submission<br>"
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\");"
for key in options:
print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, options[key])
print "pageTracker._trackPageview();"
print "} catch(err) {}</script>"
print "</BODY>"
print "</HTML>"
sys.exit(2)
#printHeader("PDB2PQR Job Submission",have_opal,jobid=resp._jobID)
pdb2pqrOpalJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalJobIDFile.write(resp._jobID)
pdb2pqrOpalJobIDFile.close()
print redirector(name)
if options.has_key("userff"):
options["userff"] = ffFileString
if options.has_key("usernames"):
options["usernames"] = namesFileString
# Recording CGI run information for PDB2PQR Opal
pdb2pqrOpalLogFile = open('%s%s%s/pdb2pqr_opal_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalLogFile.write(str(options)+'\n'+str(ff)+'\n'+str(os.environ["REMOTE_ADDR"]))
pdb2pqrOpalLogFile.close()
else:
cert = "/Users/sriramkrishnan/certs/apbs_service.cert.pem"
key = "/Users/sriramkrishnan/certs/apbs_service.privkey"
# If you are using a proxy cert, set both the cert
# and key to the location of the proxy
# Proxies have to be RFC 3820 compliant (use grid-proxy-init -rfc)
# cert = "/tmp/x509up_u506"
# key = "/tmp/x509up_u506"
# Host and port for remote services
# baseURL = proto + "://localhost:8080/"
baseURL = proto + "://ws.nbcr.net/"
# baseURL = proto + "://ws.nbcr.net:8443/"
# Retrieve a reference to the AppServicePort
appLocator = AppServiceLocator()
if proto == "http":
appServicePort = appLocator.getAppServicePort(
baseURL + "opal2/services/Pdb2pqrOpalService")
else:
if proto == "https":
# example of ssl invocation
appServicePort = appLocator.getAppServicePort(
baseURL + "opal2/services/Pdb2pqrOpalService",
ssl=1,
transdict=dict(cert_file=cert, key_file=key),
transport=httplib.HTTPSConnection)
else:
print "Unknown protocol: ", proto
sys.exit(1)
queryStatusRequest,
getOutputsRequest,
launchJobBlockingRequest,
getOutputAsBase64ByNameRequest,
)
from AppService_types import ns0
from os import mkdir
from time import sleep
from ZSI.TC import String
# Set the location of our service
# A list of NBCR services can be found at http://ws.nbcr.net/opal2/dashboard?command=serviceList
serviceURL = "http://ws.nbcr.net/opal2/services/MEME_4.4.0"
# Instantiate a new service object to interact with. Pass it the service location
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(serviceURL)
# Instantiate a new non-blocking job request
req = launchJobRequest()
# Set the command-line arguments for the job.
# Use DNA alphabet, and find 3 motifs.
req._argList = "meme crp0.fasta -dna -mod zoops -nmotifs 3"
# Get contents of local file to be used as input
fastaFile = open("./crp0.fasta", "r")
fastaFileContents = fastaFile.read()
fastaFile.close()
# Set name and content of remote input file.
def handleOpal(weboptions):
'''
Handle opal based run.
'''
# Opal-specific import statements
from AppService_client import AppServiceLocator, launchJobRequest
from AppService_types import ns0
inputFiles = []
if 'userff' in weboptions:
ffFile = ns0.InputFileType_Def('inputFile')
ffFile._name = weboptions.userfffilename
ffFile._contents = weboptions.userffstring
inputFiles.append(ffFile)
if 'usernames' in weboptions:
namesFile = ns0.InputFileType_Def('inputFile')
namesFile._name = weboptions.usernamesfilename
namesFile._contents = weboptions.usernamesstring
inputFiles.append(namesFile)
if 'ligand' in weboptions:
ligandFile = ns0.InputFileType_Def('inputFile')
ligandFile._name = weboptions.ligandfilename
ligandFile._contents = weboptions.ligandfilestring
inputFiles.append(ligandFile)
pdbOpalFile = ns0.InputFileType_Def('inputFile')
pdbOpalFile._name = weboptions.pdbfilename
pdbOpalFile._contents = weboptions.pdbfilestring
inputFiles.append(pdbOpalFile)
# launch job
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
req = launchJobRequest()
req._argList = weboptions.getCommandLine()
req._inputFile = inputFiles
try:
resp = appServicePort.launchJob(req)
except Exception as e:
printHeader("PDB2PQR Job Submission - Error")
print("<BODY>\n<P>")
print("There was an error with your job submission<br>")
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\");")
for key in weboptions:
print("pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" %
(key, weboptions[key]))
print("pageTracker._trackPageview();")
print("} catch(err) {}</script>")
print("</BODY>")
print("</HTML>")
sys.exit(2)
try:
starttime = time.time()
name = setID(starttime)
#Some job parameters logging.
os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),
'w')
apbsInputFile.write(str(weboptions["apbs"]))
apbsInputFile.close()
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),
'w')
typemapInputFile.write(str(weboptions["typemap"]))
typemapInputFile.close()
pdb2pqrOpalJobIDFile = open(
'%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalJobIDFile.write(resp._jobID)
pdb2pqrOpalJobIDFile.close()
print(redirector(name, weboptions))
# Recording CGI run information for PDB2PQR Opal
pdb2pqrOpalLogFile = open(
'%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
pdb2pqrOpalLogFile.write(
str(weboptions.getOptions()) + '\n' +
str(os.environ["REMOTE_ADDR"]))
pdb2pqrOpalLogFile.close()
except Exception as details:
print(details)
createError(name, details)
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>"
def initialize():
global _modules
if configuration.check('urlList'):
urlList = configuration.urlList.split(";")
else:
return
module_descs = []
opal_url = urlList[0]
if not opal_url:
print "ERROR: No Opal URL provided"
return
services = []
for opal_url in urlList:
if opal_url.find("/opal2") != -1:
service_list_url = opal_url + "/opalServices.xml"
opener = urllib.FancyURLopener({})
socket = opener.open(service_list_url)
text = socket.read()
feed = xml.dom.minidom.parseString(text)
for entry in feed.getElementsByTagName('entry'):
link = entry.getElementsByTagName('link')[0]
service = link.getAttribute('href')
services.append(str(service))
else:
print "ERROR: No opal2 contained in URL"
return
for url in services:
namespace = os.path.dirname(os.path.dirname(url))
servername = urlparse.urlparse(url)[1]
servername = servername.replace('.','_')
servername = servername.split(':')[0]
node_name = os.path.basename(url) + '_' + servername
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(url)
req = getAppMetadataRequest()
metadata = appServicePort.getAppMetadata(req)
if url == 'http://ws.nbcr.net/opal2/services/Pdb2pqrOpalService':
print "------------------------\n"
print metadata
print "------------------------\n"
ip_list = []
pdesc_dic = {}
try:
separator = metadata._types._taggedParams._separator
if separator == None:
separator = " "
except AttributeError:
separator = " "
try:
rawlist = metadata._types._flags._flag
for i in rawlist:
pdesc_dic[str(i._id)] = str(i._textDesc)
meta = {'url': url, 'type': 'FLAG', 'file': False, 'arg': str(i._tag), 'default': None, 'adv': True}
if i._default and str(i._default) == 'True':
meta['default'] = 'True'
ip_list.append((str(i._id), "basic:Boolean", {"defaults": str([str('True')]), "labels": str([str(i._textDesc)]), "optional": True}, meta))
else:
ip_list.append((str(i._id), "basic:Boolean", {"labels": str([str(i._textDesc)]), "optional": True}, meta))
except AttributeError:
flaglist = []
try:
rawlist = metadata._types._taggedParams._param
for i in rawlist:
#print "TAGID is " + str(i._tag)
meta = {'url': url, 'type': 'TAGGED', 'file': False, 'default': None, 'adv': True}
meta['arg'] = str(i._tag) + str(separator)
pdesc_dic[str(i._id)] = str(i._textDesc)
tagged_object = getTaggedParam(metadata, str(i._id))
if (tagged_object._paramType == 'FILE') and (tagged_object._ioType == 'INPUT'):
meta['file'] = True
if i._default:
meta['default'] = str(i._default)
ip_list.append((str(i._id), "basic:File", {"defaults": str([str(i._default)]), "labels": str([str(i._textDesc)]), "optional": True}, meta))
else:
ip_list.append((str(i._id), "basic:File", {"labels": str([str(i._textDesc)]), "optional": True}, meta))
else:
meta['file'] = False
if i._default:
meta['default'] = str(i._default)
ip_list.append((str(i._id), "basic:String", {"defaults": str([str(i._default)]), "labels": str([str(i._textDesc)]), "optional": True}, meta))
else:
ip_list.append((str(i._id), "basic:String", {"labels": str([str(i._textDesc)]), "optional": True}, meta))
except AttributeError:
taglist = []
try:
rawlist = metadata._types._untaggedParams._param
#untaglist = [str(i._id) for i in rawlist]
for i in rawlist:
meta = {'url': url, 'type': 'UNTAGGED', 'file': False, 'default': None, 'adv': True}
meta['arg'] = str(i._id)
pdesc_dic[str(i._id)] = str(i._textDesc)
untagged_object = getUntaggedParam(metadata, meta['arg'])
if (untagged_object._paramType=='FILE') and (untagged_object._ioType=='INPUT'):
meta['file'] = True
ip_list.append((str(i._id), "basic:File", {"labels": str([str(i._textDesc)]), "optional": True}, meta))
else:
if i._default:
meta['default'] = str(i._default)
ip_list.append((str(i._id), "basic:String", {"defaults": str([str(i._default)]), "labels": str([str(i._textDesc)]), "optional": True}, meta))
else:
ip_list.append((str(i._id), "basic:String", {"labels": str([str(i._textDesc)]), "optional": True}, meta))
except AttributeError:
untaglist = []
pdesc_keys = pdesc_dic.keys()
pdesc_keys.sort()
mod_doc = metadata._usage + "\n"
mod_doc += "\n***************** Input Parameters ****************\n\n"
for pk in pdesc_keys:
mod_doc += pk + ": " + pdesc_dic[pk] + "\n"
if ip_list == []:
meta = {'url': url, 'type': 'simple', 'default': None, 'adv': False}
ip_list.append(("commandLine", "basic:String", {"labels": str(["Command line arguments"]), "optional": True}, meta))
ip_list.append(("inFiles", "basic:List", {"labels": str(["Input file list"]), "optional": True}, meta))
ip_list.append(("numProcs", "basic:Integer", {"labels": str(["Number of processors"]), "optional": True}, meta))
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))
module_descs.append((node_name,
{"_inputs": get_ports(ip_list),
"_outputs": [("outurls", "basic:List")],
"_doc": mod_doc,
"namespace": namespace},
{"compute": ws_compute,
"_port_list": ip_list,
}))
# if configuration.use_b:
_modules = build_modules(module_descs)
def mainCGI():
"""
Main method for determining the query page output
"""
logopts = {}
print "Content-type: text/html\n\n"
calctype = form["calctype"].value
# prints version error, if it exists
if form["jobid"].value == 'False':
print printheader("%s Job Status Page" % calctype.upper())
progress = "version_mismatch"
runtime = 0
elif form["jobid"].value == 'notenoughmem':
print printheader("%s Job Status Page" % calctype.upper())
progress = "not_enough_memory"
runtime = 0
else:
progress = None
#Check for error html
errorpath = '%s%s%s.html' % (INSTALLDIR, TMPDIR, form["jobid"].value)
if os.path.isfile(errorpath):
string = ""
string += "<html>\n"
string += "\t<head>\n"
string += "\t\t<meta http-equiv=\"Refresh\" content=\"0; url=%s%s%s.html\">\n" % (
WEBSITE, TMPDIR, form["jobid"].value)
string += "\t</head>\n"
string += "</html>\n"
print string
return
# prepares for Opal query, if necessary
if have_opal:
if calctype == "pdb2pqr":
opal_url = PDB2PQR_OPAL_URL
elif calctype == "apbs":
opal_url = APBS_OPAL_URL
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(opal_url)
else:
appServicePort = None
# if PDB2PQR, determines if link to APBS calculation should be shown
if calctype == "pdb2pqr":
#if(form["apbsinput"].value=="True"): # change to use a file
# apbs_input = True
#else:
# apbs_input = False
apbsInputFile = open('%s%s%s/apbs_input' %
(INSTALLDIR, TMPDIR, form["jobid"].value))
apbs_input = apbsInputFile.read()
apbsInputFile.close()
if apbs_input == "True":
apbs_input = True
else:
apbs_input = False
typemapInputFile = open('%s%s%s/typemap' %
(INSTALLDIR, TMPDIR, form["jobid"].value))
typemap = typemapInputFile.read()
typemapInputFile.close()
if typemap == "True":
typemap = True
else:
typemap = False
if have_opal and progress == None:
if form["calctype"].value == "pdb2pqr":
pdb2pqrJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' %
(INSTALLDIR, TMPDIR, form["jobid"].value))
jobid = pdb2pqrJobIDFile.read()
pdb2pqrJobIDFile.close()
elif form["calctype"].value == "apbs":
apbsJobIDFile = open('%s%s%s/apbs_opal_job_id' %
(INSTALLDIR, TMPDIR, form["jobid"].value))
jobid = apbsJobIDFile.read()
apbsJobIDFile.close()
else:
jobid = form["jobid"].value
if progress == None:
cp = checkprogress(jobid, appServicePort,
calctype) # finds out status of job
progress = cp[0]
#initialize with bogus value just in case
starttime = time.time()
if progress == "running" or progress == "complete":
timefile = open(
'%s%s%s/%s_start_time' %
(INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value))
starttime = float(timefile.read())
timefile.close()
if progress == "running" or (have_opal and progress not in (
"version_mismatch", "not_enough_memory", "error", "complete")):
runtime = time.time() - starttime
elif progress == "complete":
endTimeFileString = '%s%s%s/%s_end_time' % (
INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value)
if have_opal and not os.path.isfile(endTimeFileString):
runtime = time.time() - starttime
with open(endTimeFileString, 'w') as endTimeFile:
endTimeFile.write(str(time.time()))
else:
with open(endTimeFileString, 'r') as endTimeFile:
runtime = float(endTimeFile.read()) - starttime
else:
runtime = -1
if progress == "running":
#if have_opal:
# resultsurl = cp[1]._baseURL
#else:
if calctype == "pdb2pqr":
resultsurl = '%squerystatus.cgi?jobid=%s&apbsinput=%s&calctype=pdb2pqr' % (
WEBSITE, form["jobid"].value, apbs_input)
else:
resultsurl = '%squerystatus.cgi?jobid=%s&calctype=apbs' % (
WEBSITE, form["jobid"].value)
if progress == "complete":
print printheader("%s Job Status Page" % calctype.upper(),
jobid=form["jobid"].value)
elif progress == "error":
print printheader("%s Job Status Page - Error" % calctype.upper(),
0,
jobid=form["jobid"].value)
elif progress == "running": # job is not complete, refresh in 30 seconds
print printheader("%s Job Status Page" % calctype.upper(),
refresh,
jobid=form["jobid"].value)
print "<BODY>\n<P>"
print "<h3>Status"
print "</h3>"
print "Message: %s<br />" % progress
print "Run time: %s seconds<br />" % int(runtime)
print "Current time: %s<br />" % time.asctime()
print "</P>\n<HR>\n<P>"
if progress == "complete":
if calctype == "pdb2pqr":
nexturl = 'apbs_cgi.cgi?jobid=%s' % form["jobid"].value
else:
nexturl = 'visualize.cgi?jobid=%s' % form["jobid"].value
if have_opal:
resp = appServicePort.getOutputs(getOutputsRequest(jobid))
filelist = resp._outputFile
print "Here are the results:<ul>"
print "<li>Input files<ul>"
if calctype == "pdb2pqr":
# this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension
if have_opal:
for i in range(0, len(filelist)):
if len(filelist[i]._name) == 4:
print "<li><a href=%s>%s</a></li>" % (
filelist[i]._url, filelist[i]._name)
else:
print "<li><a href=%s%s%s/%s.pdb>%s.pdb</a></li>" % (
WEBSITE, TMPDIR, jobid, jobid, jobid)
elif calctype == "apbs":
if have_opal:
for i in range(0, len(filelist)):
if filelist[i]._name == "apbsinput.in" or filelist[
i]._name[-4:] == ".pqr":
print "<li><a href=%s>%s</a></li>" % (
filelist[i]._url, filelist[i]._name)
else:
print "<li><a href=%s%s%s/apbsinput.in>apbsinput.in</a></li>" % (
WEBSITE, TMPDIR, jobid)
print "<li><a href=%s%s%s/%s.pqr>%s.pqr</a></li>" % (
WEBSITE, TMPDIR, jobid, jobid, jobid)
print "</ul></li>"
print "<li>Output files<ul>"
queryString = [str(os.environ["REMOTE_ADDR"])]
# Getting PDB2PQR run log info
if os.path.isfile('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid)):
pdb2pqrLogFile = open(
'%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid), 'r')
logstr = pdb2pqrLogFile.read().split('\n')
templogopts = eval(logstr[0])
pdb2pqrLogFile.close()
queryString.insert(0, templogopts.get('pdb', ''))
if calctype == "pdb2pqr":
if have_opal:
for i in range(0, len(filelist)):
if filelist[i]._name.endswith(
(".propka", "-typemap.html", ".pqr", ".in")):
# if filelist[i]._name[-4:]==".pqr":
# # Getting pqr file length for PDB2PQR Opal run
# f=urllib.urlopen(filelist[i]._url)
# #pqrOpalFileLength = len(f.readlines())
# f.close()
print "<li><a href=%s>%s</a></li>" % (
filelist[i]._url, filelist[i]._name)
#Get the first line of the summary file.
if filelist[i]._name.endswith(".summary"):
f = urllib.urlopen(filelist[i]._url)
summaryLine = f.readline().strip()
#logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine
queryString.append(summaryLine)
f.close()
# logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR)
else:
#Get the first line of the summary file.
summaryFile = '%s%s%s/%s%s' % (INSTALLDIR, TMPDIR, jobid,
jobid, ".summary")
if os.path.isfile(summaryFile):
with open(summaryFile) as f:
summaryLine = f.readline().strip()
#logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine
queryString.append(summaryLine)
outputfilelist = glob.glob('%s%s%s/*.propka' %
(INSTALLDIR, TMPDIR, jobid))
for i in range(0, len(outputfilelist)):
outputfilelist[i] = os.path.basename(outputfilelist[i])
for extension in ["-typemap.html", ".pqr", ".in"]:
if extension != ".in" or apbs_input != False:
if extension == "-typemap.html" and typemap == False:
continue
outputfilelist.append('%s%s' % (jobid, extension))
for outputfile in outputfilelist:
print "<li><a href=%s%s%s/%s>%s</a></li>" % (
WEBSITE, TMPDIR, jobid, outputfile, outputfile)
logopts['queryPDB2PQR'] = '|'.join(queryString)
#for extension in ["-typemap.html", ".pqr", ".in"]:
# print "<li><a href=%s%s%s/%s%s>%s%s</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, extension, jobid, extension)
elif calctype == "apbs":
if have_opal:
for i in range(0, len(filelist)):
if filelist[i]._name[-3:] == ".dx":
# compressing APBS OpenDX output files
currentpath = os.getcwd()
zipjobid = filelist[i]._name.split("-")[0]
urllib.urlretrieve(
filelist[i]._url, '%s%s%s/%s' %
(INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name))
os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, zipjobid))
# making both the dx file and the compressed file (.gz) available in the directory
syscommand = 'cp %s dxbkupfile' % (filelist[i]._name)
os.system(syscommand)
syscommand = 'gzip -9 ' + filelist[i]._name
os.system(syscommand)
syscommand = 'mv dxbkupfile %s' % (filelist[i]._name)
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = filelist[i]._name + '.gz'
print "<li><a href=%s%s%s/%s>%s</a></li>" % (
WEBSITE, TMPDIR, zipjobid, outputfilezip,
outputfilezip)
else:
outputfilelist = glob.glob('%s%s%s/%s-*.dx' %
(INSTALLDIR, TMPDIR, jobid, jobid))
for outputfile in outputfilelist:
# compressing APBS OpenDX output files
currentpath = os.getcwd()
workingpath = os.path.dirname(outputfile)
os.chdir(workingpath)
# making both the dx file and the compressed file (.gz) available in the directory
syscommand = 'cp %s dxbkupfile' % (
os.path.basename(outputfile))
os.system(syscommand)
syscommand = 'gzip -9 ' + os.path.basename(outputfile)
os.system(syscommand)
syscommand = 'mv dxbkupfile %s' % (
os.path.basename(outputfile))
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = outputfile + ".gz"
print "<li><a href=%s%s%s/%s>%s</a></li>" % (
WEBSITE, TMPDIR, jobid,
os.path.basename(outputfilezip),
os.path.basename(outputfilezip))
logopts['queryAPBS'] = '|'.join(queryString)
print "</ul></li>"
print "<li>Runtime and debugging information<ul>"
if have_opal:
stdouturl = resp._stdOut
stderrurl = resp._stdErr
else:
stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid,
calctype)
stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid,
calctype)
print "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl
print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl
print "</ul></li></ul>"
#if have_opal:
# resp = appServicePort.getOutputs(getOutputsRequest(jobid))
# for opalfile in resp._outputFile:
# if opalfile._name[-8:]!="-input.p":
# print "<li><a href=%s>%s</a></li>" % (opalfile._url, opalfile._name)
# print "<li><a href=%s>Standard output</a></li>" % (resp._stdOut)
# print "<li><a href=%s>Standard error</a></li>" % (resp._stdErr)
#else:
# for line in cp[1:]:
# line = os.path.basename(line)
# if line[-8:]!="-input.p":
# if line[-11:]=="_stdout.txt":
# printname = "Standard output"
# elif line[-11:]=="_stderr.txt":
# printname = "Standard error"
# else:
# printname = line
# print "<li><a href=%s>%s</a></li>" % (WEBSITE+TMPDIR+jobid+"/"+line,printname)
if calctype == "pdb2pqr" and apbs_input and HAVE_APBS != "":
print "</ul></p><hr><p><b><a href=%s>Click here</a> to run APBS with your results.</b></p>" % nexturl
elif calctype == "apbs":
print "</ul></p><hr><p><b><a href=%s>Click here</a> to visualize your results.</b></p>" % nexturl
elif progress == "error":
print "There was an error with your query request. This page will not refresh."
elif progress == "running":
print "Page will refresh in %d seconds<br />" % refresh
print "<HR>"
print "<small>Your results will appear at <a href=%s>this page</a>. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours).</small>" % resultsurl
elif progress == "version_mismatch":
print "The versions of APBS on the local server and on the Opal server do not match, so the calculation could not be completed"
print "</P>"
print "<script type=\"text/javascript\">"
for key in logopts:
print getEventTrackingString('queryData', key, logopts[key]),
#print "_gaq.push(['_trackPageview', '/main_cgi/has_%s_%s.html']);" % (key, logopts[key])
print "</script>"
print "</BODY>"
print "</HTML>"
def 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))