def finallyProcess(self, _edObject=None):
"""
Parses the labelit.screen log file and the generated MOSFLM script
"""
EDPluginExecProcessScript.finallyProcess(self, _edObject)
self.DEBUG("EDPluginDistlSignalStrengthThinClientv1_1.finallyProcess")
strLabelitDistlLog = self.readProcessLogFile()
if (strLabelitDistlLog is None):
strErrorMessage = "EDPluginDistlSignalStrengthThinClientv1_1.finallyProcess : Could not read the Labelit log file"
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.setImage(self.xsDataImage)
elif strLabelitDistlLog == "":
strLabelitDislErr = self.readProcessErrorLogFile()
if "httplib.BadStatusLine" in strLabelitDislErr:
strErrorMessage = "Cannot read image due to problem with file permission!"
else:
strErrorMessage = "Labelit thin client error message: " + strLabelitDislErr
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.setImage(self.xsDataImage)
else:
xsDataImageQualityIndicators = self.parseLabelitDistlOutput(strLabelitDistlLog)
xsDataImageQualityIndicators.setImage(self.xsDataImage)
xsDataResultDistlSignalStrength = XSDataResultDistlSignalStrength()
xsDataResultDistlSignalStrength.setImageQualityIndicators(xsDataImageQualityIndicators)
self.setDataOutput(xsDataResultDistlSignalStrength)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginBestv1_2.finallyProcess")
xsDataResultBest = self.getOutputDataFromDNATableFile(
os.path.join(self.getWorkingDirectory(),
self.getScriptBaseName() + "_dnaTables.xml"))
xsDataFilePathToLog = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName())))
xsDataResultBest.setPathToLogFile(xsDataFilePathToLog)
strError = self.readProcessErrorLogFile()
if ((strError is not None) and (strError != "")):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginBestv1_2.finallyProcess', 'EDPluginBestv1_2',
strError)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# Append error message to best log
strLog = self.readProcessLogFile()
strLog += "\n" + strError
EDUtilsFile.writeFile(
os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName()), strLog)
self.setDataOutput(xsDataResultBest)
self.setFailure()
else:
strPathToPlotMtv = os.path.join(
self.getWorkingDirectory(),
self.getScriptBaseName() + "_plots.mtv")
if os.path.exists(strPathToPlotMtv):
xsDataFilePathToPlotMtv = XSDataFile(
XSDataString(strPathToPlotMtv))
xsDataResultBest.setPathToPlotMtvFile(xsDataFilePathToPlotMtv)
# Check for .gle files
for strPath in os.listdir(self.getWorkingDirectory()):
if strPath.endswith(".gle"):
xsDataBestGlePlot = XSDataBestGlePlot()
xsDataBestGlePlot.script = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(), strPath)))
strDataPath = strPath[:-4] + ".dat"
if os.path.exists(
os.path.join(self.getWorkingDirectory(),
strDataPath)):
xsDataBestGlePlot.data = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
strDataPath)))
else:
strDataPath = strPath[:-4] + ".data"
if os.path.exists(
os.path.join(self.getWorkingDirectory(),
strDataPath)):
xsDataBestGlePlot.data = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
strDataPath)))
xsDataResultBest.addGlePlot(xsDataBestGlePlot)
self.setDataOutput(xsDataResultBest)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginBestv1_2.finallyProcess")
strError = self.readProcessErrorLogFile()
if ((strError is not None) and (strError != "")):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginBestv1_2.postProcess', 'EDPluginBestv1_2', strError)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setDataOutput(XSDataResultBest())
self.setFailure()
else:
xsDataResultBest = self.getOutputDataFromDNATableFile(
os.path.join(self.getWorkingDirectory(),
self.getScriptBaseName() + "_dnaTables.xml"))
xsDataFilePathToLog = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
self.getScriptLogFileName())))
xsDataResultBest.setPathToLogFile(xsDataFilePathToLog)
xsDataFilePathToPlotMtv = XSDataFile(
XSDataString(
os.path.join(self.getWorkingDirectory(),
self.getScriptBaseName() + "_plots.mtv")))
xsDataResultBest.setPathToPlotMtvFile(xsDataFilePathToPlotMtv)
self.setDataOutput(xsDataResultBest)
def finallyProcess(self, _edObject=None):
"""
Parses the labelit.screen log file and the generated MOSFLM script
"""
EDPluginExecProcessScript.finallyProcess(self, _edObject)
self.DEBUG("EDPluginDistlSignalStrengthThinClientv1_1.finallyProcess")
strLabelitDistlLog = self.readProcessLogFile()
if (strLabelitDistlLog is None):
strErrorMessage = "EDPluginDistlSignalStrengthThinClientv1_1.finallyProcess : Could not read the Labelit log file"
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.setImage(self.xsDataImage)
elif strLabelitDistlLog == "":
strLabelitDislErr = self.readProcessErrorLogFile()
if "httplib.BadStatusLine" in strLabelitDislErr:
strErrorMessage = "Cannot read image due to problem with file permission!"
else:
strErrorMessage = "Labelit thin client error message: " + strLabelitDislErr
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
xsDataImageQualityIndicators = XSDataImageQualityIndicators()
xsDataImageQualityIndicators.setImage(self.xsDataImage)
else:
xsDataImageQualityIndicators = self.parseLabelitDistlOutput(
strLabelitDistlLog)
xsDataImageQualityIndicators.setImage(self.xsDataImage)
xsDataResultDistlSignalStrength = XSDataResultDistlSignalStrength()
xsDataResultDistlSignalStrength.setImageQualityIndicators(
xsDataImageQualityIndicators)
self.setDataOutput(xsDataResultDistlSignalStrength)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginH5ToCBFv1_1.finallyProcess")
if self.CBFFile is not None:
if os.path.exists(self.CBFFile):
self.dataOutput.outputCBFFile = XSDataFile(XSDataString(self.CBFFile))
elif self.CBFFileTemplate is not None:
self.dataOutput.outputCBFFileTemplate = XSDataFile(XSDataString(self.CBFFileTemplate))
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginH5ToCBFv1_0.finallyProcess")
if self.tmpCBFFile is not None:
if os.path.exists(self.tmpCBFFile):
os.remove(self.tmpCBFFile)
if self.CBFFile is not None:
if os.path.exists(self.CBFFile):
self.dataOutput.outputCBFFile = XSDataFile(XSDataString(self.CBFFile))
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginExecMtz2Variousv1_0.finallyProcess")
xsDataResult = self.getOutputDataFromDNATableFile("rdfit.xml")
if os.path.exists(self.strScaleIntensityPlotPath):
xsDataResult.scaleIntensityPlot = XSDataFile(XSDataString(self.strScaleIntensityPlotPath))
if os.path.exists(self.strBFactorPlot):
xsDataResult.bFactorPlot = XSDataFile(XSDataString(self.strBFactorPlot))
if os.path.exists(self.htmlPagePath):
xsDataResult.htmlPage = XSDataFile(XSDataString(self.htmlPagePath))
if os.path.exists(self.jsonPath):
xsDataResult.jsonPath = XSDataFile(XSDataString(self.jsonPath))
self.setDataOutput(xsDataResult)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginBestv1_2.finallyProcess")
xsDataResultBest = self.getOutputDataFromDNATableFile(
os.path.join(self.getWorkingDirectory(), self.getScriptBaseName() + "_dnaTables.xml")
)
xsDataFilePathToLog = XSDataFile(
XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName()))
)
xsDataResultBest.setPathToLogFile(xsDataFilePathToLog)
strError = self.readProcessErrorLogFile()
if (strError is not None) and (strError != ""):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginBestv1_2.finallyProcess",
"EDPluginBestv1_2",
strError,
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
# Append error message to best log
strLog = self.readProcessLogFile()
strLog += "\n" + strError
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName()), strLog)
self.setDataOutput(xsDataResultBest)
self.setFailure()
else:
strPathToPlotMtv = os.path.join(self.getWorkingDirectory(), self.getScriptBaseName() + "_plots.mtv")
if os.path.exists(strPathToPlotMtv):
xsDataFilePathToPlotMtv = XSDataFile(XSDataString(strPathToPlotMtv))
xsDataResultBest.setPathToPlotMtvFile(xsDataFilePathToPlotMtv)
# Check for .gle files
for strPath in os.listdir(self.getWorkingDirectory()):
if strPath.endswith(".gle"):
xsDataBestGlePlot = XSDataBestGlePlot()
xsDataBestGlePlot.script = XSDataFile(
XSDataString(os.path.join(self.getWorkingDirectory(), strPath))
)
strDataPath = strPath[:-4] + ".dat"
if os.path.exists(os.path.join(self.getWorkingDirectory(), strDataPath)):
xsDataBestGlePlot.data = XSDataFile(
XSDataString(os.path.join(self.getWorkingDirectory(), strDataPath))
)
else:
strDataPath = strPath[:-4] + ".data"
if os.path.exists(os.path.join(self.getWorkingDirectory(), strDataPath)):
xsDataBestGlePlot.data = XSDataFile(
XSDataString(os.path.join(self.getWorkingDirectory(), strDataPath))
)
xsDataResultBest.addGlePlot(xsDataBestGlePlot)
self.setDataOutput(xsDataResultBest)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginExecMtz2Variousv1_0.finallyProcess")
xsDataResult = self.getOutputDataFromDNATableFile("rdfit.xml")
if os.path.exists(self.strScaleIntensityPlotPath):
xsDataResult.scaleIntensityPlot = XSDataFile(
XSDataString(self.strScaleIntensityPlotPath))
if os.path.exists(self.strBFactorPlot):
xsDataResult.bFactorPlot = XSDataFile(
XSDataString(self.strBFactorPlot))
if os.path.exists(self.htmlPagePath):
xsDataResult.htmlPage = XSDataFile(XSDataString(self.htmlPagePath))
if os.path.exists(self.jsonPath):
xsDataResult.jsonPath = XSDataFile(XSDataString(self.jsonPath))
self.setDataOutput(xsDataResult)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
EDVerbose.DEBUG("EDPluginBestv1_2.finallyProcess")
strError = self.readProcessErrorLogFile()
if((strError is not None) and (strError != "")):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginBestv1_2.postProcess', 'EDPluginBestv1_2', strError)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setDataOutput(XSDataResultBest())
self.setFailure()
else:
xsDataResultBest = self.getOutputDataFromDNATableFile(EDUtilsPath.mergePath(self.getWorkingDirectory(), self.getScriptBaseName() + "_dnaTables.xml"))
xsDataFilePathToLog = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())))
xsDataResultBest.setPathToLogFile(xsDataFilePathToLog)
self.setDataOutput(xsDataResultBest)
def finallyProcess(self, _edObject = None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginExecMtz2Variousv1_0.finallyProcess")
xsDataResult = XSDataResultMtz2Various()
xsDataResult.setHklfile(XSDataFile(XSDataString(self.strHklFile)))
self.setDataOutput(xsDataResult)
def finallyProcess(self, _edObject = None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginExecMtz2Variousv1_0.finallyProcess")
xsDataResult = self.getOutputDataFromDNATableFile("rdfit.xml")
self.setDataOutput(xsDataResult)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self, _edObject)
self.DEBUG("EDPluginPhenixXtriagev1_1.finallyProcess")
# Remove local mtz file if any
if self.strPathToLocalMtz is not None and os.path.exists(self.strPathToLocalMtz):
os.remove(self.strPathToLocalMtz)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginXOalignv1_0.finallyProcess")
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginExecMtz2Variousv1_0.finallyProcess")
xsDataResult = XSDataResultMtz2Various()
xsDataResult.setHklfile(XSDataFile(XSDataString(self.strHklFile)))
self.setDataOutput(xsDataResult)
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
self.DEBUG("EDPluginHTML2PDFv1_0.finallyProcess")
if self.pdfFile is not None:
if os.path.exists(self.pdfFile):
self.dataOutput.pdfFile = XSDataFile(XSDataString(self.pdfFile))
