def processCommandLineVersion(self):
EDVerbose.DEBUG("EDApplication.processCommandLineVersion")
if (self.__edCommandLine.existCommand(EDApplication.VERSION_PARAM_LABEL_1) or
self.__edCommandLine.existCommand(EDApplication.VERSION_PARAM_LABEL_2)):
EDVerbose.setVerboseOn()
EDVerbose.screen("%s version %s" % (self.__strName, self.__strVersion))
self.__bIsFailure = True
def processCommandLineHelp(self):
EDVerbose.DEBUG("EDApplication.processCommandLineHelp")
if (self.__edCommandLine.existCommand(EDApplication.HELP_LABEL_1)
or self.__edCommandLine.existCommand(EDApplication.HELP_LABEL_2)):
EDVerbose.setVerboseOn()
self.usage()
self.__bIsFailure = True
def processCommandLineDebugVerboseLogFile(self):
EDVerbose.DEBUG("EDApplication.processCommandLineDebugVerboseLogFile")
EDVerbose.setVerboseOff()
# Check if no log file
if (self.__edCommandLine.existCommand(EDApplication.NO_LOG_LABEL)):
EDVerbose.setLogFileOff()
EDVerbose.DEBUG("Log file output switched off")
# Check if debug mode
if (self.__edCommandLine.existCommand(EDApplication.DEBUG_PARAM_LABEL_1) or
self.__edCommandLine.existCommand(EDApplication.DEBUG_PARAM_LABEL_2)):
EDVerbose.setVerboseDebugOn()
EDVerbose.DEBUG("Debug Mode [ON]")
# Check if verbose
if (self.__edCommandLine.existCommand(EDApplication.VERBOSE_MODE_LABEL)):
EDVerbose.setVerboseOn()
from XSDataISPyBv1_4 import XSDataInputStoreAutoProc
from XSDataISPyBv1_4 import AutoProcContainer
def successAction(self, _edObject=None):
EDVerbose.screen("XML data sucessfully stored in ISPyB")
def failureAction(self, _edObject=None):
EDVerbose.ERROR("XML data not stored in ISPyB")
if __name__ == '__main__':
strCwd = os.getcwd()
strPathToTempDir = tempfile.mkdtemp(prefix="edna-autoproc2ispyb_")
os.chdir(strPathToTempDir)
EDVerbose.setVerboseOn()
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "edna.log"))
# Populate input data
EDVerbose.DEBUG("Arguments: %r" % sys.argv)
bVerbose = False
bDebug = False
listPaths = []
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
strArgPath = strArg
if os.path.dirname(strArgPath) == "":
strArgPath = os.path.join(strCwd, strArg)
def runEdnaPlugin(execPath, pluginName, isDebug, xml, additionalPaths=None):
'''
execPath - path to run plugin in
pluginName - plugin name
isDebug - True if should run edna in debug mode
xml - xml input to edna
additionalPaths - list of other python path locations
You must set EDNA_HOME to use this method
This method blocks until the EDJob has reached a final status
'''
if (not 'EDNA_HOME' in os.environ):
raise Exception("Cannot locate EDNA_HOME. Please set before running Edna plugins.")
if (not 'EDNA_SITE' in os.environ):
raise Exception(" Please set EDNA_SITE before running Edna plugins.")
'''
Add edna to path
'''
ednaKernelPath = os.environ['EDNA_HOME']+"/kernel/src"
sys.path.insert(0, ednaKernelPath)
'''
If there are any additional paths such as fabio, add these
'''
if (not additionalPaths is None and len(additionalPaths)>0):
for path in additionalPaths:
sys.path.append(path)
os.chdir(execPath)
from EDVerbose import EDVerbose
if (isDebug):
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseOn()
EDVerbose.setVerboseDebugOff()
from EDJob import EDJob
EDVerbose.setLogFileName(execPath+"/"+pluginName+".log")
edJob = EDJob(pluginName)
edJob.setDataInput(xml)
edJob.execute()
edJob.synchronize() # In theory should mean that the following loop is not needed
# Unhelpful way of waiting for EDJob to be finished
# TODO Fix this in EDJob some time
while(True):
status = edJob.getStatus()
if (status is None):
time.sleep(0.2) # 200 ms
continue
if ("failure" == status):
raise Exception("EDJob failed! ")
if ("success" == status):
break
ret = edJob.getDataOutput()
return str(ret)
from XSDataISPyBv1_3 import XSDataInputStoreAutoProc
from XSDataISPyBv1_3 import AutoProcContainer
def successAction(self, _edObject=None):
EDVerbose.screen("XML data sucessfully stored in ISPyB")
def failureAction(self, _edObject=None):
EDVerbose.ERROR("XML data not stored in ISPyB")
if __name__ == '__main__':
strCwd = os.getcwd()
strPathToTempDir = tempfile.mkdtemp(prefix="edna-autoproc2ispyb_")
os.chdir(strPathToTempDir)
EDVerbose.setVerboseOn()
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "edna.log"))
# Populate input data
EDVerbose.DEBUG("Arguments: %r" % sys.argv)
bVerbose = False
bDebug = False
listPaths = []
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
strArgPath = strArg
if os.path.dirname(strArgPath) == "":
strArgPath = os.path.join(strCwd, strArg)
def runEdnaPlugin(execPath, pluginName, isDebug, xml, additionalPaths=None):
'''
execPath - path to run plugin in
pluginName - plugin name
isDebug - True if should run edna in debug mode
xml - xml input to edna
additionalPaths - list of other python path locations
You must set EDNA_HOME to use this method
This method blocks until the EDJob has reached a final status
'''
if (not 'EDNA_HOME' in os.environ):
raise Exception(
"Cannot locate EDNA_HOME. Please set before running Edna plugins.")
if (not 'EDNA_SITE' in os.environ):
raise Exception(" Please set EDNA_SITE before running Edna plugins.")
'''
Add edna to path
'''
ednaKernelPath = os.environ['EDNA_HOME'] + "/kernel/src"
sys.path.insert(0, ednaKernelPath)
'''
If there are any additional paths such as fabio, add these
'''
if (not additionalPaths is None and len(additionalPaths) > 0):
for path in additionalPaths:
sys.path.append(path)
os.chdir(execPath)
from EDVerbose import EDVerbose
if (isDebug):
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseOn()
EDVerbose.setVerboseDebugOff()
from EDJob import EDJob
EDVerbose.setLogFileName(execPath + "/" + pluginName + ".log")
edJob = EDJob(pluginName)
edJob.setDataInput(xml)
edJob.execute()
edJob.synchronize(
) # In theory should mean that the following loop is not needed
# Unhelpful way of waiting for EDJob to be finished
# TODO Fix this in EDJob some time
while (True):
status = edJob.getStatus()
if (status is None):
time.sleep(0.2) # 200 ms
continue
if ("failure" == status):
raise Exception("EDJob failed! ")
if ("success" == status):
break
ret = edJob.getDataOutput()
return str(ret)
