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))