def postProcess(self, _edObject=None):
"""
postProcess of the plugin EDPluginSPDCorrectv10.py:
- convert to HDF if needed (to be implemented)
- move images (if needed)
- set result XML
"""
EDPluginExecProcess.postProcess(self)
self.DEBUG("EDPluginSPDCorrectv10.postProcess")
EDUtilsPath.createFolder(self.dictGeometry["OutputDir"])
if self.getClassName() == "EDPluginSPDCorrectv10":
strInputImagePathNoSfx = os.path.splitext(os.path.basename(self.pathToInputFile))[0]
destFileBaseName = strInputImagePathNoSfx + self.dictGeometry["OutputFileType"]
strOutputFilePath = os.path.join(self.dictGeometry["OutputDir"], destFileBaseName)
if not self._bFireAndForget:
if "corrected" in self.dictRes:
strTempFilePath = self.dictRes["corrected"]
else:
strTempFilePath = os.path.join(self.getWorkingDirectory(), destFileBaseName)
if self.dictGeometry["OutputFileType"].lower() in [".hdf5", ".nexus", ".h5", ".nx"]:
self.WARNING("HDF5/Nexus output is not yet implemented in the SPD plugin.")
if os.path.exists(strOutputFilePath):
self.WARNING("Destination file exists, I will leave result file in %s." % strTempFilePath)
strOutputFilePath = strTempFilePath
else:
shutil.move(strTempFilePath, strOutputFilePath)
# # Create the output data
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(strOutputFilePath))
xsDataResultSPD = XSDataResultSPD()
xsDataResultSPD.setCorrectedFile(xsDataFile)
self.setDataOutput(xsDataResultSPD)
def postProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Checks that the installed 3rd party software is in the list of compatible versions
"""
EDPluginExecProcess.postProcess(self)
self.DEBUG("EDPluginExecProcessScript.postProcess")
# Tests the compatibles executable versions
listCompatibleVersions = self.getListOfCompatibleVersions()
if (len(listCompatibleVersions) != 0):
bFound = False
for compatibleVersion in listCompatibleVersions:
bFound = self.findStringInLog(compatibleVersion)
if (bFound == True):
break
if (bFound == False):
strErrorMessage = "Plugin not compatible with %s, compatible versions are: %s" % (
self.getStringVersion(),
self.getCompatibleVersionsStringLine())
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
def postProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Checks that the installed 3rd party software is in the list of compatible versions
"""
EDPluginExecProcess.postProcess(self)
self.DEBUG("EDPluginExecProcessScript.postProcess")
# Tests the compatibles executable versions
listCompatibleVersions = self.getListOfCompatibleVersions()
if(len(listCompatibleVersions) != 0):
bFound = False
for compatibleVersion in listCompatibleVersions:
bFound = self.findStringInLog(compatibleVersion)
if(bFound == True):
break
if(bFound == False):
strErrorMessage = "Plugin not compatible with %s, compatible versions are: %s" % (self.getStringVersion(), self.getCompatibleVersionsStringLine())
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError, strErrorMessage
def preProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Generates the script
"""
EDPluginExecProcess.preProcess(self)
self.DEBUG("EDPluginExecProcessScript.preProcess")
# The generateScript method will be called at the end of the preProcess method
self.connectPreProcess(self.generateScript)
def preProcess(self, _edObject=None):
"""
Calls the parent preProcess method
Generates the script
"""
EDPluginExecProcess.preProcess(self)
self.DEBUG("EDPluginExecProcessScript.preProcess")
# The generateScript method will be called at the end of the preProcess method
self.connectPreProcess(self.generateScript)
def preProcess(self, _edObject=None):
"""
Preprocess methods for the EDPluginSPDCorrectv10 :
- Reads input parameters
- Creates the displacement matrix if the the detector is tilted
- create the configuration for SPD
- selects the worker (SPD program under control)
"""
EDPluginExecProcess.preProcess(self)
self.DEBUG("EDPluginSPDCorrectv10.preProcess")
# Check that the input data and correction images are present
self.getInputParameter()
if "SpatialDistortionFile" in self.dictGeometry:
splineDM = Spline()
splineDM.read(self.dictGeometry["SpatialDistortionFile"])
self.dictGeometry["PixelSizeX"], self.dictGeometry[
"PixelSizeY"] = splineDM.getPixelSize()
else:
splineDM = None
if self.dictGeometry["AngleOfTilt"] != 0:
EDPluginSPDCorrectv10.__lockTilt.acquire()
if splineDM == None:
edfFile = fabio.open(self.pathToInputFile)
data = edfFile.data
size = data.shape
splineDM = splineDM.zeros(xmin=0.0,
ymin=0.0,
xmax=size[0],
ymax=size[1])
if ("PixelSizeX"
in self.dictGeometry) and ("PixelSizeY"
in self.dictGeometry):
splineDM.setPixelSize = (self.dictGeometry["PixelSizeX"],
self.dictGeometry["PixelSizeY"])
strtmp = os.path.join(
self.getSPDCommonDirectory(),
os.path.basename(
os.path.splitext(
self.dictGeometry["SpatialDistortionFile"])[0]))
if not (os.path.isfile(strtmp + "-tilted-x.edf")
and os.path.isfile(strtmp + "-tilted-y.edf")):
# self.DEBUG("preProcess: \t EDPluginSPDCorrectv10.__lock.acquire(), currently: %i" % EDPluginSPDCorrectv10.__lock._Semaphore__value)
if not (os.path.isfile(strtmp + "-tilted-x.edf")
and os.path.isfile(strtmp + "-tilted-y.edf")):
#The second test is just here to gain some time as the global semaphore could be in use elsewhere
self.createDisplacementMatrix(splineDM)
self.dictGeometry["DistortionFileX"] = strtmp + "-tilted-x.edf"
self.dictGeometry["DistortionFileY"] = strtmp + "-tilted-y.edf"
EDPluginSPDCorrectv10.__lockTilt.release()
self.generateSPDCommand()
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 postProcess(self, _edObject=None):
"""
postProcess of the plugin EDPluginSPDCorrectv10.py:
- convert to HDF if needed (to be implemented)
- move images (if needed)
- set result XML
"""
EDPluginExecProcess.postProcess(self)
self.DEBUG("EDPluginSPDCorrectv10.postProcess")
EDUtilsPath.createFolder(self.dictGeometry["OutputDir"])
if self.getClassName() == "EDPluginSPDCorrectv10":
strInputImagePathNoSfx = os.path.splitext(
os.path.basename(self.pathToInputFile))[0]
destFileBaseName = strInputImagePathNoSfx + self.dictGeometry[
"OutputFileType"]
strOutputFilePath = os.path.join(self.dictGeometry["OutputDir"],
destFileBaseName)
if not self._bFireAndForget:
if "corrected" in self.dictRes:
strTempFilePath = self.dictRes["corrected"]
else:
strTempFilePath = os.path.join(self.getWorkingDirectory(),
destFileBaseName)
if self.dictGeometry["OutputFileType"].lower() in [
".hdf5", ".nexus", ".h5", ".nx"
]:
self.WARNING(
"HDF5/Nexus output is not yet implemented in the SPD plugin."
)
if os.path.exists(strOutputFilePath):
self.WARNING(
"Destination file exists, I will leave result file in %s."
% strTempFilePath)
strOutputFilePath = strTempFilePath
else:
shutil.move(strTempFilePath, strOutputFilePath)
# # Create the output data
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(strOutputFilePath))
xsDataResultSPD = XSDataResultSPD()
xsDataResultSPD.setCorrectedFile(xsDataFile)
self.setDataOutput(xsDataResultSPD)
def preProcess(self, _edObject=None):
"""
Preprocess methods for the EDPluginSPDCorrectv10 :
- Reads input parameters
- Creates the displacement matrix if the the detector is tilted
- create the configuration for SPD
- selects the worker (SPD program under control)
"""
EDPluginExecProcess.preProcess(self)
self.DEBUG("EDPluginSPDCorrectv10.preProcess")
# Check that the input data and correction images are present
self.getInputParameter()
if "SpatialDistortionFile" in self.dictGeometry:
splineDM = Spline()
splineDM.read(self.dictGeometry["SpatialDistortionFile"])
self.dictGeometry["PixelSizeX"], self.dictGeometry["PixelSizeY"] = splineDM.getPixelSize()
else:
splineDM = None
if self.dictGeometry["AngleOfTilt"] != 0:
EDPluginSPDCorrectv10.__lockTilt.acquire()
if splineDM == None:
edfFile = fabio.open(self.pathToInputFile)
data = edfFile.data
size = data.shape
splineDM = splineDM.zeros(xmin=0.0, ymin=0.0, xmax=size[0], ymax=size[1])
if ("PixelSizeX" in self.dictGeometry) and ("PixelSizeY" in self.dictGeometry):
splineDM.setPixelSize = (self.dictGeometry["PixelSizeX"], self.dictGeometry["PixelSizeY"])
strtmp = os.path.join(
self.getSPDCommonDirectory(),
os.path.basename(os.path.splitext(self.dictGeometry["SpatialDistortionFile"])[0]),
)
if not (os.path.isfile(strtmp + "-tilted-x.edf") and os.path.isfile(strtmp + "-tilted-y.edf")):
# self.DEBUG("preProcess: \t EDPluginSPDCorrectv10.__lock.acquire(), currently: %i" % EDPluginSPDCorrectv10.__lock._Semaphore__value)
if not (os.path.isfile(strtmp + "-tilted-x.edf") and os.path.isfile(strtmp + "-tilted-y.edf")):
# The second test is just here to gain some time as the global semaphore could be in use elsewhere
self.createDisplacementMatrix(splineDM)
self.dictGeometry["DistortionFileX"] = strtmp + "-tilted-x.edf"
self.dictGeometry["DistortionFileY"] = strtmp + "-tilted-y.edf"
EDPluginSPDCorrectv10.__lockTilt.release()
self.generateSPDCommand()
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 __init__ (self):
"""
Initializes process related attributes described above
"""
EDPluginExecProcess.__init__(self)
self.__strConfigShell = "/bin/bash"
self.__strScriptExecutor = None
self.__strScriptExecutable = None
self.__strConfigSetupCCP4 = None
self.__strVersion = None
self.__listCompatibleVersions = []
self.__strScriptCommandline = ""
self.__strScriptBaseName = None
self.__strScriptLogFileName = None
self.__strScriptErrorLogFileName = None
self.__strScriptFileName = None
self.__bRequireCCP4 = False
self.__listCommandPreExecution = []
self.__listCommandExecution = []
self.__listCommandPostExecution = []
self.__iPollScriptProcessTime = 1 # [s]
self.__strPathToHostNamePidFile = None
self.__iNumberOfLastLinesFromLogFileIfError = 15
def __init__(self):
"""
Initializes process related attributes described above
"""
EDPluginExecProcess.__init__(self)
self.__strConfigShell = "/bin/bash"
self.__strScriptExecutor = None
self.__strScriptExecutable = None
self.__strConfigSetupCCP4 = None
self.__strVersion = None
self.__listCompatibleVersions = []
self.__strScriptCommandline = ""
self.__strScriptBaseName = None
self.__strScriptLogFileName = None
self.__strScriptErrorLogFileName = None
self.__strScriptFileName = None
self.__bRequireCCP4 = False
self.__listCommandPreExecution = []
self.__listCommandExecution = []
self.__listCommandPostExecution = []
self.__iPollScriptProcessTime = 1 # [s]
self.__strPathToHostNamePidFile = None
self.__iNumberOfLastLinesFromLogFileIfError = 15
def __init__(self):
"""
Constructor of the plugin: just do some simple initialization
"""
EDPluginExecProcess.__init__(self)
# self.DEBUG(self.getBaseName())
if self.getClassName() == "EDPluginSPDCorrectv10":
self.setXSDataInputClass(XSDataInputSPD)
self.dictGeometry = {}
self.dictRes = {}
self.xsDataInputSPD = None
self.pathToInputFile = None
self._SPDconfig = None
self.worker = None
self.workerID = None
self._listCompatibleVersions = []
self._strConfigExecutable = None
self.bTimeOut = False
self._iConfigNumberOfWorker = 0
self._bFireAndForget = False
self.strCurrentVersion = None
self.addCompatibleVersion("spd version SPD = 1.2 SAXS = 2.436 EDF = 2.171")
def __init__(self):
"""
Constructor of the plugin: just do some simple initialization
"""
EDPluginExecProcess.__init__(self)
# self.DEBUG(self.getBaseName())
if self.getClassName() == "EDPluginSPDCorrectv10":
self.setXSDataInputClass(XSDataInputSPD)
self.dictGeometry = {}
self.dictRes = {}
self.xsDataInputSPD = None
self.pathToInputFile = None
self._SPDconfig = None
self.worker = None
self.workerID = None
self._listCompatibleVersions = []
self._strConfigExecutable = None
self.bTimeOut = False
self._iConfigNumberOfWorker = 0
self._bFireAndForget = False
self.strCurrentVersion = None
self.addCompatibleVersion("spd version SPD = 1.2 SAXS = 2.436 EDF = 2.171")
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
"""
EDPluginExecProcess.configure(self)
self.DEBUG("EDPluginExecProcessScript.configure")
strShell = self.config.get(self.CONF_EXEC_PROCESS_SCRIPT_SHELL)
if strShell is None:
self.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
self.CONF_EXEC_PROCESS_SCRIPT_SHELL + ", using default value: " + self.getScriptShell())
else:
self.setScriptShell(strShell)
strScriptExecutor = self.config.get(
self.CONF_EXEC_PROCESS_SCRIPT_EXECUTOR)
if strScriptExecutor is None:
self.setScriptExecutor(self.getScriptShell())
self.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
self.CONF_EXEC_PROCESS_SCRIPT_EXECUTOR + ", using script shell: " + self.getScriptShell())
else:
self.setScriptExecutor(strScriptExecutor)
if self.__strScriptExecutable is None:
strScriptExecutable = self.config.get(
self.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE)
if strScriptExecutable is None:
strErrorMessage = "Configuration parameter %s missing for plugin %s with EDNA_SITE=%s" % \
(self.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE, \
self.getPluginName(), EDUtilsPath.EDNA_SITE)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
else:
# Check that the executable file exists
if not os.path.exists(strScriptExecutable):
strErrorMessage = "Cannot find configured executable %s: %s for plugin %s with EDNA_SITE=%s" % \
(self.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE, strScriptExecutable, \
self.getPluginName(), EDUtilsPath.EDNA_SITE)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
else:
self.setScriptExecutable(strScriptExecutable)
if not self.__strScriptExecutable:
self.error("No executable found for plugin %s with EDNA_SITE=%s" %
(self.getClassName(), EDUtilsPath.EDNA_SITE))
strConfigSetupCCP4 = self.config.get(
self.CONF_EXEC_PROCESS_SCRIPT_SETUP_CCP4)
if strConfigSetupCCP4 is None:
self.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
self.CONF_EXEC_PROCESS_SCRIPT_SETUP_CCP4 + ", NO default value!")
else:
self.setSetupCCP4(strConfigSetupCCP4)
strVersion = self.config.get(
self.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING)
if strVersion is None:
self.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
self.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING + ", NO default value!")
else:
self.setStringVersion(strVersion)
if self.__strScriptBaseName is None:
self.setScriptBaseName(self.getBaseName())
if self.__strScriptFileName is None:
self.setScriptFileName(self.__strScriptBaseName + ".sh")
if self.__strScriptLogFileName is None:
self.setScriptLogFileName(self.__strScriptBaseName + ".log")
if self.__strScriptErrorLogFileName is None:
self.setScriptErrorLogFileName(self.__strScriptBaseName + ".err")
if self.__strScriptExecutable is not None:
self.__strPathToHostNamePidFile = os.path.join(
self.getWorkingDirectory(),
os.path.basename(self.__strScriptExecutable) +
"_hostNamePid.txt")
def process(self, _edObject=None):
"""
This method starts the execution of the EDNA script using EDActionExecuteSystemCommand
In case of failure, an error message is added to the list and the plugin fails.
"""
EDPluginExecProcess.process(self)
self.DEBUG("EDPluginExecProcessScript.process starting")
self.synchronizeOn()
if "TIMEOUT" in EDUtilsFile.readFile(self.__strPathToHostNamePidFile):
self.error("Timeout message found in %s" %
self.__strPathToHostNamePidFile)
self.hasTimedOut(True)
bTimeOut = self.isTimeOut()
if bTimeOut == True:
self.DEBUG(
"EDPluginExecProcessScript.process ========================================= ERROR! ================"
)
strErrorMessage = "%s execution timed out ( > %.1f s)!" % (
self.__strScriptExecutable, float(self.getTimeOut()))
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
strExecutionStatus = "timeout"
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
else:
strExecutionStatus = self.getExecutionStatus()
# Report an error if the result is not "0" and the result is not an empty string
if not strExecutionStatus == "0" and not strExecutionStatus == "":
self.DEBUG(
"EDPluginExecProcessScript.process ========================================= ERROR! ================"
)
# Add any messages in the error log file (.err) to the list of error messages
strErrorLog = self.readProcessErrorLogFile()
if strErrorLog is None:
strErrorMessage = "%s execution error - status : %s" % (
self.getClassName(), strExecutionStatus)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
else:
strErrorMessage = "%s execution error : %s" % (
self.getClassName(), strErrorLog)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
# Add any messages in the log file (.log) to the list of error messages
strLog = self.readProcessLogFile()
if strLog is not None:
# Cut down the log file to the last part if it's long
listLogLines = strLog.split("\n")
if len(listLogLines
) > self.__iNumberOfLastLinesFromLogFileIfError:
strErrorMessage = "Last part of the %s log file:" % self.__strScriptExecutable
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
listLogLastLines = listLogLines[
-self.__iNumberOfLastLinesFromLogFileIfError:]
strLogLastLines = ""
for strLine in listLogLastLines:
strLogLastLines += strLine + "\n"
self.ERROR(strLogLastLines)
self.addErrorMessage(strLogLastLines)
strMessage = "Please inspect log file: %s" % os.path.join(
self.getWorkingDirectory(),
self.getScriptLogFileName())
self.ERROR(strMessage)
self.addErrorMessage(strMessage)
else:
strMessage = "%s log file: \n%s" % (
self.__strScriptExecutable, strLog)
self.ERROR(strMessage)
self.addErrorMessage(strMessage)
# Save the return code of the external program in the PID file
open(self.__strPathToHostNamePidFile,
"a").write(strExecutionStatus + os.linesep)
self.DEBUG("EDPluginExecProcessScript.process finished ")
self.synchronizeOff()
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
"""
EDPluginExecProcess.configure(self)
EDVerbose.DEBUG("EDPluginExecProcessScript.configure")
xsPluginItem = self.getConfiguration()
if (xsPluginItem == None):
EDVerbose.warning("EDPluginExecProcessScript.configure: No plugin item defined.")
xsPluginItem = XSPluginItem()
strShell = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_SHELL)
if(strShell == None):
EDVerbose.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_SHELL + ", using default value: " + self.getScriptShell())
else:
self.setScriptShell(strShell)
strScriptExecutor = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTOR)
if(strScriptExecutor == None):
self.setScriptExecutor(self.getScriptShell())
EDVerbose.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTOR + ", using script shell: " + self.getScriptShell())
else:
self.setScriptExecutor(strScriptExecutor)
if (self.getScriptExecutable() is None):
strScriptExecutable = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE)
if(strScriptExecutable == None):
strErrorMessage = "Configuration parameter missing: " + EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_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(strScriptExecutable) == False):
strErrorMessage = "Cannot find configured " + EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE + " : " + strScriptExecutable
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if (EDVerbose.isVerboseDebug()):
raise RuntimeError, strErrorMessage
else:
self.setScriptExecutable(strScriptExecutable)
strConfigSetupCCP4 = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_SETUP_CCP4)
if(strConfigSetupCCP4 == None):
EDVerbose.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_SETUP_CCP4 + ", NO default value!")
else:
self.setSetupCCP4(strConfigSetupCCP4)
strVersion = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING)
if(strVersion == None):
EDVerbose.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
EDPluginExecProcessScript.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING + ", NO default value!")
else:
self.setStringVersion(strVersion)
if (self.__strScriptBaseName == None):
self.setScriptBaseName(self.getBaseName())
if (self.__strScriptFileName == None):
self.setScriptFileName(self.__strScriptBaseName + ".sh")
if (self.__strScriptLogFileName == None):
self.setScriptLogFileName(self.__strScriptBaseName + ".log")
if (self.__strScriptErrorLogFileName == None):
self.setScriptErrorLogFileName(self.__strScriptBaseName + ".err")
self.__strPathToHostNamePidFile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.__strScriptExecutable) + "_hostNamePid.txt")
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
"""
EDPluginExecProcess.configure(self)
self.DEBUG("EDPluginExecProcessScript.configure")
strShell = self.config.get(self.CONF_EXEC_PROCESS_SCRIPT_SHELL)
if strShell is None:
self.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
self.CONF_EXEC_PROCESS_SCRIPT_SHELL + ", using default value: " + self.getScriptShell())
else:
self.setScriptShell(strShell)
strScriptExecutor = self.config.get(self.CONF_EXEC_PROCESS_SCRIPT_EXECUTOR)
if strScriptExecutor is None:
self.setScriptExecutor(self.getScriptShell())
self.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
self.CONF_EXEC_PROCESS_SCRIPT_EXECUTOR + ", using script shell: " + self.getScriptShell())
else:
self.setScriptExecutor(strScriptExecutor)
if self.__strScriptExecutable is None:
strScriptExecutable = self.config.get(self.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE)
if strScriptExecutable is None:
strErrorMessage = "Configuration parameter %s missing for plugin %s with EDNA_SITE=%s" % \
(self.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE, \
self.getPluginName(), EDUtilsPath.EDNA_SITE)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError, strErrorMessage
else:
# Check that the executable file exists
if not os.path.exists(strScriptExecutable):
strErrorMessage = "Cannot find configured executable %s: %s for plugin %s with EDNA_SITE=%s" % \
(self.CONF_EXEC_PROCESS_SCRIPT_EXECUTABLE, strScriptExecutable, \
self.getPluginName(), EDUtilsPath.EDNA_SITE)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError, strErrorMessage
else:
self.setScriptExecutable(strScriptExecutable)
if not self.__strScriptExecutable:
self.error("No executable found for plugin %s with EDNA_SITE=%s" % (self.getClassName(), EDUtilsPath.EDNA_SITE))
strConfigSetupCCP4 = self.config.get(self.CONF_EXEC_PROCESS_SCRIPT_SETUP_CCP4)
if strConfigSetupCCP4 is None:
self.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
self.CONF_EXEC_PROCESS_SCRIPT_SETUP_CCP4 + ", NO default value!")
else:
self.setSetupCCP4(strConfigSetupCCP4)
strVersion = self.config.get(self.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING)
if strVersion is None:
self.DEBUG("EDPluginExecProcessScript.configure: No configuration parameter found for: " + \
self.CONF_EXEC_PROCESS_SCRIPT_VERSION_STRING + ", NO default value!")
else:
self.setStringVersion(strVersion)
if self.__strScriptBaseName is None:
self.setScriptBaseName(self.getBaseName())
if self.__strScriptFileName is None:
self.setScriptFileName(self.__strScriptBaseName + ".sh")
if self.__strScriptLogFileName is None:
self.setScriptLogFileName(self.__strScriptBaseName + ".log")
if self.__strScriptErrorLogFileName is None:
self.setScriptErrorLogFileName(self.__strScriptBaseName + ".err")
if self.__strScriptExecutable is not None:
self.__strPathToHostNamePidFile = os.path.join(self.getWorkingDirectory(), os.path.basename(self.__strScriptExecutable) + "_hostNamePid.txt")
def process(self, _edObject=None):
"""
This method starts the execution of the EDNA script using EDActionExecuteSystemCommand
In case of failure, an error message is added to the list and the plugin fails.
"""
EDPluginExecProcess.process(self)
self.DEBUG("EDPluginExecProcessScript.process starting")
self.synchronizeOn()
if "TIMEOUT" in EDUtilsFile.readFile(self.__strPathToHostNamePidFile):
self.error("Timeout message found in %s" % self.__strPathToHostNamePidFile)
self.hasTimedOut(True)
bTimeOut = self.isTimeOut()
if bTimeOut == True:
self.DEBUG("EDPluginExecProcessScript.process ========================================= ERROR! ================")
strErrorMessage = "%s execution timed out ( > %.1f s)!" % (self.__strScriptExecutable, float(self.getTimeOut()))
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
strExecutionStatus = "timeout"
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
else:
strExecutionStatus = self.getExecutionStatus()
# Report an error if the result is not "0" and the result is not an empty string
if not strExecutionStatus == "0" and not strExecutionStatus == "":
self.DEBUG("EDPluginExecProcessScript.process ========================================= ERROR! ================")
# Add any messages in the error log file (.err) to the list of error messages
strErrorLog = self.readProcessErrorLogFile()
if strErrorLog is None:
strErrorMessage = "%s execution error - status : %s" % (self.getClassName(), strExecutionStatus)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
else:
strErrorMessage = "%s execution error : %s" % (self.getClassName(), strErrorLog)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if self.isVerboseDebug():
raise RuntimeError(strErrorMessage)
# Add any messages in the log file (.log) to the list of error messages
strLog = self.readProcessLogFile()
if strLog is not None:
# Cut down the log file to the last part if it's long
listLogLines = strLog.split("\n")
if len(listLogLines) > self.__iNumberOfLastLinesFromLogFileIfError:
strErrorMessage = "Last part of the %s log file:" % self.__strScriptExecutable
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
listLogLastLines = listLogLines[-self.__iNumberOfLastLinesFromLogFileIfError:]
strLogLastLines = ""
for strLine in listLogLastLines:
strLogLastLines += strLine + "\n"
self.ERROR(strLogLastLines)
self.addErrorMessage(strLogLastLines)
strMessage = "Please inspect log file: %s" % os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())
self.ERROR(strMessage)
self.addErrorMessage(strMessage)
else:
strMessage = "%s log file: \n%s" % (self.__strScriptExecutable, strLog)
self.ERROR(strMessage)
self.addErrorMessage(strMessage)
# Save the return code of the external program in the PID file
open(self.__strPathToHostNamePidFile, "a").write(strExecutionStatus + os.linesep)
self.DEBUG("EDPluginExecProcessScript.process finished ")
self.synchronizeOff()
