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)
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)
# Make remote invocation to get application metadata
print "Getting Application Metadata"
req = getAppMetadataRequest()
resp = appServicePort.getAppMetadata(req)
print "Usage:", resp._usage
# Set up remote job launch
req = launchJobRequest()
req._argList = "-ipdb benzene.pdb -h -opdb output.pdb"
inputFiles = []
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name ='benzene.pdb'
sampleFile = open("./etc/benzene.pdb", "r")
sampleFileString = sampleFile.read()
sampleFile.close()
inputFile._contents = sampleFileString
inputFiles.append(inputFile)
req._inputFile = inputFiles
def getServiceMetadata(self):
""" """
req = getAppMetadataRequest()
resp = self.appServicePort.getAppMetadata(req)
return resp
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 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 getServiceMetadata(self):
""" return the XML appConfig used by this application """
req = getAppMetadataRequest()
resp = self.appServicePort.getAppMetadata(req)
return resp
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)
