def _initBlast(self, program, db, queryName, querySeq, evalue, matrix,
passes):
self.program = program
self.db = db
self.queryName = queryName
self.params = (querySeq, evalue, matrix, passes)
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
inputFile = ns0.InputFileType_Def("inputFile")
inputFile._name = "query.fa"
inputFile._contents = self.makeFasta(queryName, querySeq)
service = "BlastproteinServicePort"
argList = "-P %s -d %s -i %s -o %s -e %s -M %s -p %s" % (
program, db, inputFile._name, self.outputFile, evalue, matrix,
passes)
try:
self.opal = OpalService(service)
except:
import traceback, sys
print "Traceback from Blast request:"
traceback.print_exc(file=sys.stdout)
print """
Typically, if you get a TypeError, it's a problem on the remote server
and it should be fixed shortly. If you get a different error or
get TypeError consistently for more than a day, please report the
problem using the Report a Bug... entry in the Help menu. Please
include the traceback printed above as part of the problem description."""
from chimera import NonChimeraError
raise NonChimeraError("Blast web service appears "
"to be down. See Reply Log "
"for more details.")
self.opal.launchJob(argList, _inputFile=[inputFile])
from chimera.tasks import Task
self.task = Task(self._title(), self.cancelCB, self.statusCB)
def _initSession(self, program, db, queryName, params, running, opalData):
self.program = program
self.db = db
self.queryName = queryName
self.params = params
from WebServices.opal_client import OpalService
self.opal = OpalService(sessionData=opalData)
if not running:
self.task = None
else:
from chimera.tasks import Task
self.task = Task(self._title(), self.cancelCB, self.statusCB)
def _getWebService(residue): from WebServices.AppService_types import ns0 from WebServices.opal_client import OpalService service = "ccd_catServicePort" argList = "%s" % residue opal = OpalService(service) status, fileMap = opal.launchJobBlocking(argList) opal.destroy() if not status: return None import urllib2 f = urllib2.urlopen(fileMap["stdout.txt"]) data = f.read() f.close() return data
def _getWebService(residue):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
service = "ccd_catServicePort"
argList = "%s" % residue
opal = OpalService(service)
status, fileMap = opal.launchJobBlocking(argList)
opal.destroy()
if not status:
return None
import urllib2
f = urllib2.urlopen(fileMap["stdout.txt"])
data = f.read()
f.close()
return data
def _initBlast(self, program, db, queryName, querySeq,
evalue, matrix, passes):
self.program = program
self.db = db
self.queryName = queryName
self.params = (querySeq, evalue, matrix, passes)
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
inputFile = ns0.InputFileType_Def("inputFile")
inputFile._name = "query.fa"
inputFile._contents = self.makeFasta(queryName, querySeq)
service = "BlastproteinServicePort"
argList = "-P %s -d %s -i %s -o %s -e %s -M %s -p %s" % (
program, db, inputFile._name,
self.outputFile, evalue, matrix, passes)
try:
self.opal = OpalService(service)
except:
import traceback, sys
print "Traceback from Blast request:"
traceback.print_exc(file=sys.stdout)
print """
Typically, if you get a TypeError, it's a problem on the remote server
and it should be fixed shortly. If you get a different error or
get TypeError consistently for more than a day, please report the
problem using the Report a Bug... entry in the Help menu. Please
include the traceback printed above as part of the problem description."""
from chimera import NonChimeraError
raise NonChimeraError("Blast web service appears "
"to be down. See Reply Log "
"for more details.")
self.opal.launchJob(argList, _inputFile=[inputFile])
from chimera.tasks import Task
self.task = Task(self._title(), self.cancelCB,
self.statusCB)
def __init__(self, queryName, querySeq, evalue, matrix, finishCB):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
self.queryName = queryName
inputFile = ns0.InputFileType_Def("inputFile")
inputFile._name = "query.fa"
inputFile._contents = self.makeFasta(queryName, querySeq)
service = "BlastpdbServicePort"
argList = "-i %s -o %s -e %s -M %s" % (self.inputFile._name,
self.outputFile, evalue, matrix)
self.opal = OpalService(service)
self.opal.launchJob(argList, _inputFile=[inputFile])
self.finishCB = finishCB
from chimera.tasks import Task
self.task = Task("blastpdb %s" % queryName, self.cancelCB,
self.statusCB)
def __init__(self, pdbpath, expath, name, fig):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
self.pdbpath = pdbpath
self.expath = expath
self.name = name
self.figure = fig
pdbFile = ns0.InputFileType_Def("inputFile")
pdbFile._name = "pdbfile"
f = open(pdbpath)
pdbFile._contents = f.read()
f.close()
files = [pdbFile]
argList = "pdbfile"
if expath:
exFile = ns0.InputFileType_Def("inputFile")
exFile._name = "exfile"
f = open(expath)
exFile._contents = f.read()
f.close()
files.append(exFile)
argList += " exfile"
try:
self.opal = OpalService("SAXSService")
except:
import traceback, sys
print "Traceback from SAXS request:"
traceback.print_exc(file=sys.stdout)
print """
Typically, if you get a TypeError, it's a problem on the remote server
and it should be fixed shortly. If you get a different error or
get TypeError consistently for more than a day, please report the
problem using the Report a Bug... entry in the Help menu. Please
include the traceback printed above as part of the problem description."""
from chimera import NonChimeraError
raise NonChimeraError("SAXS web service appears "
"to be down. See Reply Log "
"for more details.")
self.opal.launchJob(argList, _inputFile=files)
from chimera.tasks import Task
self.task = Task("SAXS " + self.name, self.cancelCB, self.statusCB)
def _initSession(self, program, db, queryName, params, running, opalData): self.program = program self.db = db self.queryName = queryName self.params = params from WebServices.opal_client import OpalService self.opal = OpalService(sessionData=opalData) if not running: self.task = None else: from chimera.tasks import Task self.task = Task(self._title(), self.cancelCB, self.statusCB)
def __init__(self, queryName, querySeq, evalue, matrix, finishCB):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
self.queryName = queryName
inputFile = ns0.InputFileType_Def("inputFile")
inputFile._name = "query.fa"
inputFile._contents = self.makeFasta(queryName, querySeq)
service = "BlastpdbServicePort"
argList = "-i %s -o %s -e %s -M %s" % (
self.inputFile._name, self.outputFile,
evalue, matrix)
self.opal = OpalService(service)
self.opal.launchJob(argList, _inputFile=[inputFile])
self.finishCB = finishCB
from chimera.tasks import Task
self.task = Task("blastpdb %s" % queryName, self.cancelCB,
self.statusCB)
def __init__(self, pdbpath, expath, name, fig):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
self.pdbpath = pdbpath
self.expath = expath
self.name = name
self.figure = fig
pdbFile = ns0.InputFileType_Def("inputFile")
pdbFile._name = "pdbfile"
f = open(pdbpath)
pdbFile._contents = f.read()
f.close()
files = [ pdbFile ]
argList = "pdbfile"
if expath:
exFile = ns0.InputFileType_Def("inputFile")
exFile._name = "exfile"
f = open(expath)
exFile._contents = f.read()
f.close()
files.append(exFile)
argList += " exfile"
try:
self.opal = OpalService("SAXSService")
except:
import traceback, sys
print "Traceback from SAXS request:"
traceback.print_exc(file=sys.stdout)
print """
Typically, if you get a TypeError, it's a problem on the remote server
and it should be fixed shortly. If you get a different error or
get TypeError consistently for more than a day, please report the
problem using the Report a Bug... entry in the Help menu. Please
include the traceback printed above as part of the problem description."""
from chimera import NonChimeraError
raise NonChimeraError("SAXS web service appears "
"to be down. See Reply Log "
"for more details.")
self.opal.launchJob(argList, _inputFile=files)
from chimera.tasks import Task
self.task = Task("SAXS " + self.name, self.cancelCB, self.statusCB)
class BlastproteinService:
outputFile = "blast.out"
def __init__(self, finishCB, params=None, sessionData=None):
self.finishCB = finishCB
if params is not None:
self._initBlast(*params)
else:
self._initSession(*sessionData)
def _initBlast(self, program, db, queryName, querySeq, evalue, matrix,
passes):
self.program = program
self.db = db
self.queryName = queryName
self.params = (querySeq, evalue, matrix, passes)
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
inputFile = ns0.InputFileType_Def("inputFile")
inputFile._name = "query.fa"
inputFile._contents = self.makeFasta(queryName, querySeq)
service = "BlastproteinServicePort"
argList = "-P %s -d %s -i %s -o %s -e %s -M %s -p %s" % (
program, db, inputFile._name, self.outputFile, evalue, matrix,
passes)
try:
self.opal = OpalService(service)
except:
import traceback, sys
print "Traceback from Blast request:"
traceback.print_exc(file=sys.stdout)
print """
Typically, if you get a TypeError, it's a problem on the remote server
and it should be fixed shortly. If you get a different error or
get TypeError consistently for more than a day, please report the
problem using the Report a Bug... entry in the Help menu. Please
include the traceback printed above as part of the problem description."""
from chimera import NonChimeraError
raise NonChimeraError("Blast web service appears "
"to be down. See Reply Log "
"for more details.")
self.opal.launchJob(argList, _inputFile=[inputFile])
from chimera.tasks import Task
self.task = Task(self._title(), self.cancelCB, self.statusCB)
def _initSession(self, program, db, queryName, params, running, opalData):
self.program = program
self.db = db
self.queryName = queryName
self.params = params
from WebServices.opal_client import OpalService
self.opal = OpalService(sessionData=opalData)
if not running:
self.task = None
else:
from chimera.tasks import Task
self.task = Task(self._title(), self.cancelCB, self.statusCB)
def _title(self):
return "%s %s: %s" % (self.program, self.db, self.queryName)
def sessionData(self):
return (self.program, self.db, self.queryName, self.params, self.task
is not None, self.opal.sessionData())
def cancelCB(self):
self.task = None
def statusCB(self):
self.task.updateStatus(self.opal.currentStatus())
if not self.opal.isFinished():
self.opal.queryStatus()
return
self.task = None
fileMap = self.opal.getOutputs()
if self.opal.isFinished() > 0:
# Successful completion
self.finishCB(self.getURLContent(fileMap[self.outputFile]))
else:
# Failed
from chimera import replyobj
replyobj.error("blast %s failed; "
"see Reply Log for more information\n" %
self.queryName)
self.showURLContent("blast stderr", fileMap["stderr.txt"])
self.showURLContent("blast stdout", fileMap["stdout.txt"])
def makeFasta(self, name, seq):
output = [">QUERY\n"]
maxLine = 60
for i in range(0, len(seq), maxLine):
end = min(i + maxLine, len(seq))
output.append("%s\n" % seq[i:end])
return ''.join(output)
def getURLContent(self, url):
import urllib2
f = urllib2.urlopen(url)
data = f.read()
f.close()
return data
def showURLContent(self, title, url):
from chimera import replyobj
data = self.getURLContent(url)
replyobj.message("%s\n-----\n%s-----\n" % (title, data))
class BlastpdbService:
outputFile = "blast.out"
def __init__(self, queryName, querySeq, evalue, matrix, finishCB):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
self.queryName = queryName
inputFile = ns0.InputFileType_Def("inputFile")
inputFile._name = "query.fa"
inputFile._contents = self.makeFasta(queryName, querySeq)
service = "BlastpdbServicePort"
argList = "-i %s -o %s -e %s -M %s" % (self.inputFile._name,
self.outputFile, evalue, matrix)
self.opal = OpalService(service)
self.opal.launchJob(argList, _inputFile=[inputFile])
self.finishCB = finishCB
from chimera.tasks import Task
self.task = Task("blastpdb %s" % queryName, self.cancelCB,
self.statusCB)
def cancelCB(self):
self.task = None
def statusCB(self):
self.task.updateStatus(self.opal.currentStatus())
if not self.opal.isFinished():
self.opal.queryStatus()
return
self.task = None
fileMap = self.opal.getOutputs()
if self.opal.isFinished() > 0:
# Successful completion
self.finishCB(self.getURLContent(fileMap[self.outputFile]))
else:
# Failed
from chimera import replyobj
replyobj.error("blastpdb %s failed; "
"see Reply Log for more information" %
self.queryName)
try:
self.showURLContent("blastpdb stdout", fileMap["stdout"])
except KeyError:
pass
try:
self.showURLContent("blastpdb stderr", fileMap["stderr"])
except KeyError:
pass
def makeFasta(self, name, seq):
output = [">QUERY\n"]
maxLine = 60
for i in range(0, len(seq), maxLine):
end = min(i + maxLine, len(seq))
output.append("%s\n" % seq[i:end])
return ''.join(output)
def getURLContent(self, url):
import urllib2
f = urllib2.urlopen(url)
data = f.read()
f.close()
return data
def showURLContent(self, title, url):
from chimera import replyobj
data = self.getURLContent(url)
replyobj.message("%s\n-----\n%s-----\n" % (title, data))
class BlastproteinService:
outputFile = "blast.out"
def __init__(self, finishCB, params=None, sessionData=None):
self.finishCB = finishCB
if params is not None:
self._initBlast(*params)
else:
self._initSession(*sessionData)
def _initBlast(self, program, db, queryName, querySeq,
evalue, matrix, passes):
self.program = program
self.db = db
self.queryName = queryName
self.params = (querySeq, evalue, matrix, passes)
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
inputFile = ns0.InputFileType_Def("inputFile")
inputFile._name = "query.fa"
inputFile._contents = self.makeFasta(queryName, querySeq)
service = "BlastproteinServicePort"
argList = "-P %s -d %s -i %s -o %s -e %s -M %s -p %s" % (
program, db, inputFile._name,
self.outputFile, evalue, matrix, passes)
try:
self.opal = OpalService(service)
except:
import traceback, sys
print "Traceback from Blast request:"
traceback.print_exc(file=sys.stdout)
print """
Typically, if you get a TypeError, it's a problem on the remote server
and it should be fixed shortly. If you get a different error or
get TypeError consistently for more than a day, please report the
problem using the Report a Bug... entry in the Help menu. Please
include the traceback printed above as part of the problem description."""
from chimera import NonChimeraError
raise NonChimeraError("Blast web service appears "
"to be down. See Reply Log "
"for more details.")
self.opal.launchJob(argList, _inputFile=[inputFile])
from chimera.tasks import Task
self.task = Task(self._title(), self.cancelCB,
self.statusCB)
def _initSession(self, program, db, queryName,
params, running, opalData):
self.program = program
self.db = db
self.queryName = queryName
self.params = params
from WebServices.opal_client import OpalService
self.opal = OpalService(sessionData=opalData)
if not running:
self.task = None
else:
from chimera.tasks import Task
self.task = Task(self._title(), self.cancelCB,
self.statusCB)
def _title(self):
return "%s %s: %s" % (self.program, self.db, self.queryName)
def sessionData(self):
return (self.program, self.db, self.queryName, self.params,
self.task is not None,
self.opal.sessionData())
def cancelCB(self):
self.task = None
def statusCB(self):
self.task.updateStatus(self.opal.currentStatus())
if not self.opal.isFinished():
self.opal.queryStatus()
return
self.task = None
fileMap = self.opal.getOutputs()
if self.opal.isFinished() > 0:
# Successful completion
self.finishCB(self.getURLContent(
fileMap[self.outputFile]))
else:
# Failed
from chimera import replyobj
replyobj.error("blast %s failed; "
"see Reply Log for more information\n"
% self.queryName)
self.showURLContent("blast stderr", fileMap["stderr.txt"])
self.showURLContent("blast stdout", fileMap["stdout.txt"])
def makeFasta(self, name, seq):
output = [ ">QUERY\n" ]
maxLine = 60
for i in range(0, len(seq), maxLine):
end = min(i + maxLine, len(seq))
output.append("%s\n" % seq[i:end])
return ''.join(output)
def getURLContent(self, url):
import urllib2
f = urllib2.urlopen(url)
data = f.read()
f.close()
return data
def showURLContent(self, title, url):
from chimera import replyobj
data = self.getURLContent(url)
replyobj.message("%s\n-----\n%s-----\n" % (title, data))
class BlastpdbService:
outputFile = "blast.out"
def __init__(self, queryName, querySeq, evalue, matrix, finishCB):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
self.queryName = queryName
inputFile = ns0.InputFileType_Def("inputFile")
inputFile._name = "query.fa"
inputFile._contents = self.makeFasta(queryName, querySeq)
service = "BlastpdbServicePort"
argList = "-i %s -o %s -e %s -M %s" % (
self.inputFile._name, self.outputFile,
evalue, matrix)
self.opal = OpalService(service)
self.opal.launchJob(argList, _inputFile=[inputFile])
self.finishCB = finishCB
from chimera.tasks import Task
self.task = Task("blastpdb %s" % queryName, self.cancelCB,
self.statusCB)
def cancelCB(self):
self.task = None
def statusCB(self):
self.task.updateStatus(self.opal.currentStatus())
if not self.opal.isFinished():
self.opal.queryStatus()
return
self.task = None
fileMap = self.opal.getOutputs()
if self.opal.isFinished() > 0:
# Successful completion
self.finishCB(self.getURLContent(
fileMap[self.outputFile]))
else:
# Failed
from chimera import replyobj
replyobj.error("blastpdb %s failed; "
"see Reply Log for more information"
% self.queryName)
try:
self.showURLContent("blastpdb stdout",
fileMap["stdout"])
except KeyError:
pass
try:
self.showURLContent("blastpdb stderr",
fileMap["stderr"])
except KeyError:
pass
def makeFasta(self, name, seq):
output = [ ">QUERY\n" ]
maxLine = 60
for i in range(0, len(seq), maxLine):
end = min(i + maxLine, len(seq))
output.append("%s\n" % seq[i:end])
return ''.join(output)
def getURLContent(self, url):
import urllib2
f = urllib2.urlopen(url)
data = f.read()
f.close()
return data
def showURLContent(self, title, url):
from chimera import replyobj
data = self.getURLContent(url)
replyobj.message("%s\n-----\n%s-----\n" % (title, data))
class ProfileOpalService:
def __init__(self, pdbpath, expath, name, fig):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
self.pdbpath = pdbpath
self.expath = expath
self.name = name
self.figure = fig
pdbFile = ns0.InputFileType_Def("inputFile")
pdbFile._name = "pdbfile"
f = open(pdbpath)
pdbFile._contents = f.read()
f.close()
files = [ pdbFile ]
argList = "pdbfile"
if expath:
exFile = ns0.InputFileType_Def("inputFile")
exFile._name = "exfile"
f = open(expath)
exFile._contents = f.read()
f.close()
files.append(exFile)
argList += " exfile"
try:
self.opal = OpalService("SAXSService")
except:
import traceback, sys
print "Traceback from SAXS request:"
traceback.print_exc(file=sys.stdout)
print """
Typically, if you get a TypeError, it's a problem on the remote server
and it should be fixed shortly. If you get a different error or
get TypeError consistently for more than a day, please report the
problem using the Report a Bug... entry in the Help menu. Please
include the traceback printed above as part of the problem description."""
from chimera import NonChimeraError
raise NonChimeraError("SAXS web service appears "
"to be down. See Reply Log "
"for more details.")
self.opal.launchJob(argList, _inputFile=files)
from chimera.tasks import Task
self.task = Task("SAXS " + self.name, self.cancelCB, self.statusCB)
def cancelCB(self):
self.task = None
def statusCB(self):
self.task.updateStatus(self.opal.currentStatus())
if not self.opal.isFinished():
self.opal.queryStatus()
return
self.task = None
self.filemap = self.opal.getOutputs()
if self.opal.isFinished() > 0:
# Successful completion
self.finished()
else:
# Failed
from chimera import replyobj
replyobj.error("SAXS %s failed; see Reply Log for more information"
% self.name)
self.showFileContent("stdout.txt")
self.showFileContent("stderr.txt")
def finished(self):
if self.expath:
data = self.getFileContent("pdbfile_exfile.dat")
p = read_profile_data(data, 3)
else:
data = self.getFileContent("pdbfile.dat")
p = read_profile_data(data, 2)
self.figure = plot_profile(p, self.name, self.figure)
def getURLContent(self, url):
import urllib2
f = urllib2.urlopen(url)
data = f.read()
f.close()
return data
def getFileContent(self, filename):
return self.getURLContent(self.filemap[filename])
def showURLContent(self, title, url):
from chimera import replyobj
data = self.getURLContent(url)
replyobj.message("%s\n-----\n%s-----\n" % (title, data))
def showFileContent(self, filename):
try:
url = self.filemap[filename]
except KeyError:
from chimera import replyobj
replyobj.message("SAXS profile: there is no file named \"%s\"" % filename)
else:
self.showURLContent("SAXS profile %s" % filename, url)
class ProfileOpalService:
def __init__(self, pdbpath, expath, name, fig):
from WebServices.AppService_types import ns0
from WebServices.opal_client import OpalService
self.pdbpath = pdbpath
self.expath = expath
self.name = name
self.figure = fig
pdbFile = ns0.InputFileType_Def("inputFile")
pdbFile._name = "pdbfile"
f = open(pdbpath)
pdbFile._contents = f.read()
f.close()
files = [pdbFile]
argList = "pdbfile"
if expath:
exFile = ns0.InputFileType_Def("inputFile")
exFile._name = "exfile"
f = open(expath)
exFile._contents = f.read()
f.close()
files.append(exFile)
argList += " exfile"
try:
self.opal = OpalService("SAXSService")
except:
import traceback, sys
print "Traceback from SAXS request:"
traceback.print_exc(file=sys.stdout)
print """
Typically, if you get a TypeError, it's a problem on the remote server
and it should be fixed shortly. If you get a different error or
get TypeError consistently for more than a day, please report the
problem using the Report a Bug... entry in the Help menu. Please
include the traceback printed above as part of the problem description."""
from chimera import NonChimeraError
raise NonChimeraError("SAXS web service appears "
"to be down. See Reply Log "
"for more details.")
self.opal.launchJob(argList, _inputFile=files)
from chimera.tasks import Task
self.task = Task("SAXS " + self.name, self.cancelCB, self.statusCB)
def cancelCB(self):
self.task = None
def statusCB(self):
self.task.updateStatus(self.opal.currentStatus())
if not self.opal.isFinished():
self.opal.queryStatus()
return
self.task = None
self.filemap = self.opal.getOutputs()
if self.opal.isFinished() > 0:
# Successful completion
self.finished()
else:
# Failed
from chimera import replyobj
replyobj.error(
"SAXS %s failed; see Reply Log for more information" %
self.name)
self.showFileContent("stdout.txt")
self.showFileContent("stderr.txt")
def finished(self):
if self.expath:
data = self.getFileContent("pdbfile_exfile.dat")
p = read_profile_data(data, 3)
else:
data = self.getFileContent("pdbfile.dat")
p = read_profile_data(data, 2)
self.figure = plot_profile(p, self.name, self.figure)
def getURLContent(self, url):
import urllib2
f = urllib2.urlopen(url)
data = f.read()
f.close()
return data
def getFileContent(self, filename):
return self.getURLContent(self.filemap[filename])
def showURLContent(self, title, url):
from chimera import replyobj
data = self.getURLContent(url)
replyobj.message("%s\n-----\n%s-----\n" % (title, data))
def showFileContent(self, filename):
try:
url = self.filemap[filename]
except KeyError:
from chimera import replyobj
replyobj.message("SAXS profile: there is no file named \"%s\"" %
filename)
else:
self.showURLContent("SAXS profile %s" % filename, url)