def configure(self):
"""
Here we override the EDPluginExecProcessScript.configure method BEFORE calling it.
we define especially the executable that should come from the input-XML and not from the Site-XML.
This is the main difference with EDPluginExecProcessScript.
The configure method modifies also the stdout from .log to .out ... if we are re-using stdout for the result
"""
self.DEBUG("EDPluginExecCommandLinev10.configure")
self.setScriptExecutable(self.dataInput.commandLineProgram.path.value)
if self.dataInput.getCommandLineOptions() :
strOptions = self.dataInput.getCommandLineOptions().value + " " + self.dataInput.inputFileName.path.value
else:
strOptions = self.dataInput.inputFileName.path
self.setScriptCommandline(strOptions)
xsPluginItem = XSPluginItem()
self.setConfiguration(xsPluginItem)
if self.dataInput.getOutfileFromStdout() is not None:
if self.dataInput.getOutfileFromStdout().value :
if (self.getScriptBaseName() == None):
self.setScriptBaseName(self.getBaseName())
if (self.getScriptLogFileName() == None):
self.setScriptLogFileName(self.getScriptBaseName() + ".out")
# And finally we call the configure method of the parent.
EDPluginExecProcessScript.configure(self)
def configure(self):
"""
Configures the plugin from the configuration file with the following parameters:
- CONF_MAX_THREAD max number of threads in the action cluster
- CONF_FILE_SIZE minimum file size
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginBioSaxsToSASv1_0.configure")
if (self.__class__.size is None) or (self.__class__.maxThreads is None):
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
self.warning("EDPluginBioSaxsToSASv1_0.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
conf_size = self.config.get(self.CONF_FILE_SIZE, None)
if conf_size is None:
strMessage = 'EDPluginBioSaxsToSASv1_0.configure: Configuration parameter missing: \
%s for %s, defaulting to "1000"' % (self.CONF_FILE_SIZE, EDUtilsPath.EDNA_SITE)
self.WARNING(strMessage)
self.addErrorWarningMessagesToExecutiveSummary(strMessage)
self.__class__.size = 1000
else:
self.__class__.size = int(conf_size)
maxThreads = self.config.get(self.CONF_MAX_THREAD, None)
if maxThreads is None:
strMessage = 'EDPluginBioSaxsToSASv1_0.configure: Configuration parameter missing: \
%s for %s, defaulting to "max"' % (self.CONF_MAX_THREAD, EDUtilsPath.EDNA_SITE)
self.WARNING(strMessage)
self.addErrorWarningMessagesToExecutiveSummary(strMessage)
self.__class__.maxThreads = None
else:
self.__class__.maxThreads = int(maxThreads)
def testSetXSConfigurationItem(self):
xsPluginItem = XSPluginItem()
xsPluginItem.name = "EDPluginTestSetConfig"
edConfiguration = EDConfiguration()
edConfiguration.setXSConfigurationItem(xsPluginItem)
xsDataPluginItem = edConfiguration.getXSConfigurationItem(
"EDPluginTestSetConfig")
EDAssert.equal(True, xsDataPluginItem is not None,
"Obtanied set configuration")
def getXSConfigurationItem(self, _strPluginName):
"Method offering compatibility with XML structure: deprecated !!!"
config = None
if _strPluginName in self._dictPluginConfiguration:
config = self._dictPluginConfiguration[_strPluginName]
else: # Try to load "project" configuration
config = self.get(_strPluginName)
if config is not None:
return XSPluginItem(name=_strPluginName,
XSParamList=XSParamList([
XSParamItem(name=i, value=str(config[i]))
for i in config
]))
def configure(self):
"""
setup two configurations:
--> MAX_OFFSET_VALUE
--> FILL_VALUE
"""
EDPluginExec.configure(self)
if not self.__class__.CONFIGURED:
with self.__class__._clsLock:
if not self.__class__.CONFIGURED:
self.DEBUG("EDPluginExecShiftImagev1_1.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
self.WARNING(
"EDPluginExecShiftImagev1_1.configure: No plugin item defined."
)
xsPluginItem = XSPluginItem()
strFill = EDConfiguration.getStringParamValue(
xsPluginItem, self.__class__.FILL_KEY)
if (strFill == None):
self.WARNING("EDPluginExecShiftImagev1_1.configure: No configuration parameter found for: %s using default value: %s\n%s"\
% (self.FILL_KEY, self.FILL_VALUE, xsPluginItem.marshal()))
else:
strFill = strFill.strip().lower()
if strFill in ["min", "max", "mean"]:
self.__class__.FILL_VALUE = strFill
else:
try:
self.__class__.FILL_VALUE = float(strFill)
except ValueError, error:
self.ERROR(
"unable to convert %s to float: %s" %
(strFill, error))
strMaxOffset = EDConfiguration.getStringParamValue(
xsPluginItem, self.__class__.MAX_OFFSET_KEY)
if (strMaxOffset == None):
self.WARNING("EDPluginExecShiftImagev1_1.configure: No configuration parameter found for: %s using default value: %s\n%s"\
% (self.MAX_OFFSET_KEY, self.MAX_OFFSET_VALUE, xsPluginItem.marshal()))
else:
if strMaxOffset.isdigit():
try:
self.__class__.MAX_OFFSET_VALUE = int(
strMaxOffset)
except ValueError, error:
self.ERROR("unable to convert %s to int: %s" %
(strMaxOffset, error))
else:
self.WARNING("EDPluginExecShiftImagev1_1.configure: No configuration parameter found for: %s using default value: %s\n%s"\
% (self.MAX_OFFSET_KEY, self.MAX_OFFSET_VALUE, xsPluginItem.marshal()))
def configure(self):
"""
Configures the plugin from the configuration file with the following parameters
- Script executable to be invoked
- number of worker
- The 3rd party executable installed version
"""
EDPluginExecProcess.configure(self)
self.DEBUG(" EDPluginSPDCorrect.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
self.WARNING(
"EDPluginSPDCorrect.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
if (self.getExecutable() is None):
edStringScriptExecutable = EDConfiguration.getStringParamValue(
xsPluginItem, CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE)
if (edStringScriptExecutable == None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginSPDCorrect.process', self.getClassName(), "Configuration parameter missing: " \
+ CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Check that the executable file exists
if not os.path.isfile(edStringScriptExecutable):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginSPDCorrect.process', self.getClassName(), "Cannot find configured " \
+ CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE + " : " + edStringScriptExecutable)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
self.setExecutable(edStringScriptExecutable)
edStringConfigSetupNbWorker = EDConfiguration.getStringParamValue(
xsPluginItem, CONF_EXEC_MAX_MAX_NUMBER_OF_WORKERS)
if (edStringConfigSetupNbWorker == None):
self.DEBUG(
"EDPluginSPDCorrect.configure: No configuration parameter found for: "
+ CONF_EXEC_MAX_MAX_NUMBER_OF_WORKERS + ", NO default value!")
else:
self._iConfigNumberOfWorker = int(edStringConfigSetupNbWorker)
edStringVersion = EDConfiguration.getStringParamValue(
xsPluginItem, CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING)
if (edStringVersion == None):
self.DEBUG(
"EDPluginSPDCorrect.configure: No configuration parameter found for: "
+ CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING +
", NO default value!")
else:
self.setStringVersion(edStringVersion)
def configure(self):
EDPluginExecProcessScript.configure(self)
self.DEBUG("EDPluginControlLabelitv10.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
self.warning("EDPluginControlLabelitv10.configure: No Labelit plugin item defined.")
xsPluginItem = XSPluginItem()
strPathToLabelitSetpathScript = EDConfiguration.getStringParamValue(xsPluginItem, self.strCONF_PATH_TO_LABELIT_SETPATH_SCRIPT)
if(strPathToLabelitSetpathScript == None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlLabelitv10.configure', self.getClassName(), "Configuration parameter missing: " + self.strCONF_PATH_TO_LABELIT_SETPATH_SCRIPT)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
self.setPathToLabelitSetpathScript(strPathToLabelitSetpathScript)
def configure(self):
EDPluginExecProcessScript.configure(self)
self.DEBUG("EDPluginLabelitv1_1.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
self.warning("EDPluginLabelitv1_1.configure: No Labelit plugin item defined.")
xsPluginItem = XSPluginItem()
strPathToLabelitSetpathScript = EDConfiguration.getStringParamValue(xsPluginItem, \
EDPluginLabelitv1_1.CONF_PATH_TO_LABELIT_SETPATH_SCRIPT)
if(strPathToLabelitSetpathScript == None):
strErrorMessage = "EDPluginLabelitv1_1.configure : Configuration parameter missing: " + \
EDPluginLabelitv1_1.CONF_PATH_TO_LABELIT_SETPATH_SCRIPT
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
self.setPathToLabelitSetpathScript(strPathToLabelitSetpathScript)
def configure(self):
"""
Configures the plugin from the configuration file with the following parameters
- Excpected image size
"""
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlDiffractionCTv1_2.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning("EDPluginControlDiffractionCTv1_2.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
strImageSize = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginControlDiffractionCTv1_2.CONF_INPUT_IMAGE_SIZE)
if(strImageSize == None):
EDVerbose.WARNING("EDPluginControlDiffractionCTv1_2.configure: No configuration parameter found for: %s, using default value: %s " % (\
EDPluginControlDiffractionCTv1_2.CONF_INPUT_IMAGE_SIZE, self.iImageSize))
else:
self.iImageSize = int(strImageSize)
def configure(self):
"""
Configures the plugin from the configuration file with the following parameters:
- DummyPixelValue: the value to be assigned to dummy pixels.
"""
EDPluginControl.configure(self)
self.DEBUG("EDPluginBioSaxsNormalizev1_1.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
self.warning("EDPluginBioSaxsNormalizev1_1.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
self.dummy = EDConfiguration.getStringParamValue(xsPluginItem, self.CONF_DUMMY_PIXEL_VALUE)
if self.dummy is None:
strMessage = 'EDPluginBioSaxsNormalizev1_1.configure: %s Configuration parameter missing: \
%s, defaulting to "-1"' % (self.getBaseName(), self.CONF_DUMMY_PIXEL_VALUE)
self.WARNING(strMessage)
self.addErrorWarningMessagesToExecutiveSummary(strMessage)
self.dummy = -1
def configure(self):
"""
Add the dtype to the configuration file, probably "float32" or "float64"
"""
EDPluginExec.configure(self)
self.DEBUG("EDPluginExecNormalizeImagev1_1.configure")
if self.__class__.dtype is None:
with self.__class__.semaphore:
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
self.WARNING("EDPluginExecNormalizeImagev1_1.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
strDtype = EDConfiguration.getStringParamValue(xsPluginItem, self.CONF_DTYPE_KEY)
if(strDtype == None):
self.WARNING("EDPluginExecNormalizeImagev1_1.configure: No configuration parameter found for: %s using default value: %s\n%s"\
% (self.CONF_DTYPE_KEY, self.CONF_DTYPE_DEFAULT, xsPluginItem.marshal()))
self.__class__.dtype = self.CONF_DTYPE_DEFAULT
else:
self.__class__.dtype = str(strDtype.strip().lower())
def configure(self):
"""
Configures the plugin from the configuration file with the following parameters
- The CONVOLUTION method
"""
EDPluginExec.configure(self)
if self.CONF_CONVOLUTION is None:
with self.__class__.__sem:
self.DEBUG("EDPluginExecMeasureOffsetv1_0.configure")
xsPluginItem = self.getConfiguration()
if xsPluginItem is None:
self.WARNING(
"EDPluginExecMeasureOffsetv1_0.configure: No plugin item defined."
)
xsPluginItem = XSPluginItem()
strCONVOLUTION = EDConfiguration.getStringParamValue(
xsPluginItem, self.CONF_CONVOLUTION_KEY)
if strCONVOLUTION is None:
self.WARNING("EDPluginExecMeasureOffsetv1_0.configure: No configuration parameter found for: %s using default value: %s\n%s"\
% (self.CONF_CONVOLUTION_KEY, self.CONF_CONVOLUTION_DEFAULT, xsPluginItem.marshal()))
self.__class__CONF_CONVOLUTION = self.CONF_CONVOLUTION_DEFAULT
else:
self.__class__.CONF_CONVOLUTION = strCONVOLUTION.strip(
).lower()
def configure(self):
"""
Configures the plugin from the configuration file with the following
parameters
- The shell that will execute the script
- Script executor
- Script executable to be invoked
- Path to CCP4 setup file if required
- The 3rd party executable installed version
"""
EDPluginExec.configure(self)
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning(
"EDPluginExecProcessXIA2CORE.configure: No plugin item defined."
)
xsPluginItem = XSPluginItem()
if (self.getExecutable() is None):
strExecutable = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE)
if (strExecutable == None):
strErrorMessage = "Configuration parameter missing: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
# Check that the executable file exists
if (os.path.exists(strExecutable) == False):
strErrorMessage = "Cannot find configured " + EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_EXECUTABLE + " : " + strExecutable
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
self.setExecutable(strExecutable)
if (self.getConfigXIA2COREType() is None):
strXIA2COREType = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_XIA2CORE_TYPE)
if (strXIA2COREType == None):
strErrorMessage = "Configuration parameter not set: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_XIA2CORE_TYPE
EDVerbose.DEBUG(strErrorMessage)
else:
# FIXME test that this is a legal name
self.__strConfigXIA2COREType = strXIA2COREType
strVersion = EDConfiguration.getStringParamValue(
xsPluginItem,
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_VERSION_STRING)
if (strVersion == None):
EDVerbose.DEBUG("EDPluginExecProcessXIA2CORE.configure: No configuration parameter found for: " + \
EDPluginExecProcessXIA2CORE.CONF_EXEC_PROCESS_VERSION_STRING + ", NO default value!")
else:
self.setStringVersion(strVersion)
if (self.__strLogFileName == None):
self.setLogFileName(self.getBaseName() + ".log")
if (self.__strErrorLogFileName == None):
self.setErrorLogFileName(self.getBaseName() + ".err")
if self.__strExecutable is None:
EDVerbose.ERROR("Executable not defined in configuration file")
# shall we raise an exception?
self.__strPathToHostNamePidFile = os.path.join(
self.getWorkingDirectory(),
os.path.basename(self.__strExecutable) + "_hostNamePid.txt")
return