def storeResultsInISPyB(self, _strSubject, _strMessage):
strSubject = _strSubject
strMessage = _strMessage
xsDataResultCharacterisation = self.edPluginControlInterface.getDataOutput(
).getResultCharacterisation()
self.xsDataResultMXCuBE.setCharacterisationResult(
xsDataResultCharacterisation)
xsDataResultControlISPyB = self.edPluginControlInterface.getDataOutput(
).getResultControlISPyB()
if xsDataResultControlISPyB != None:
self.xsDataResultMXCuBE.setScreeningId(
xsDataResultControlISPyB.getScreeningId())
if xsDataResultCharacterisation != None:
self.xsDataResultMXCuBE.characterisationResult = xsDataResultCharacterisation
strPathCharacterisationResult = os.path.join(
self.getWorkingDirectory(), "CharacterisationResult.xml")
xsDataResultCharacterisation.exportToFile(
strPathCharacterisationResult)
self.xsDataResultMXCuBE.setListOfOutputFiles(
XSDataString(strPathCharacterisationResult))
# For the moment, create "DNA" style output directory
strPathToDNAFileDirectory = self.createDNAFileDirectoryPath(
xsDataResultCharacterisation)
xsDataDictionaryLogFile = None
if not EDUtilsPath.isALBA:
if (self.createDNAFileDirectory(strPathToDNAFileDirectory)):
xsDataDictionaryLogFile = self.createOutputFileDictionary(
xsDataResultCharacterisation,
strPathToDNAFileDirectory)
strPyArchPathToDNAFileDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(
strPathToDNAFileDirectory)
if (self.createDNAFileDirectory(strPyArchPathToDNAFileDirectory)):
xsDataDictionaryLogFile = self.createOutputFileDictionary(
xsDataResultCharacterisation,
strPyArchPathToDNAFileDirectory)
self.xsDataResultMXCuBE.setOutputFileDictionary(
xsDataDictionaryLogFile)
if xsDataResultCharacterisation.getStatusMessage():
strMessage += "\n\n"
strMessage += xsDataResultCharacterisation.getStatusMessage(
).getValue()
if xsDataResultCharacterisation.getShortSummary():
strMessage += "\n\n"
strMessage += xsDataResultCharacterisation.getShortSummary(
).getValue()
self.sendEmail(strSubject, strMessage)
# Fix for bug EDNA-55 : If burning strategy EDNA2html shouldn't be run
bRunExecOutputHTML = False
xsDataInputMXCuBE = self.getDataInput()
xsDataDiffractionPlan = xsDataInputMXCuBE.getDiffractionPlan()
if xsDataDiffractionPlan.getStrategyOption() is not None:
strStrategyOption = xsDataDiffractionPlan.getStrategyOption(
).getValue()
if strStrategyOption.find("-DamPar") != -1:
bRunExecOutputHTML = False
if (self.edPluginExecOutputHTML
is not None) and bRunExecOutputHTML:
self.edPluginExecOutputHTML.setDataInput(
XSDataFile(XSDataString(strPathToDNAFileDirectory)),
"dnaFileDirectory")
self.edPluginExecOutputHTML.execute()
# Fix for bug MXSUP-251: Put the BEST .par file in the EDNA characterisation root directory
xsDataIntegrationResult = xsDataResultCharacterisation.getIntegrationResult(
)
if xsDataIntegrationResult:
listXSDataIntegrationSubWedgeResult = xsDataIntegrationResult.getIntegrationSubWedgeResult(
)
for xsDataIntegrationSubWedgeResult in listXSDataIntegrationSubWedgeResult:
if xsDataIntegrationSubWedgeResult.getBestfilePar(
) is not None:
strBestfilePar = xsDataIntegrationSubWedgeResult.getBestfilePar(
).getValue()
# Put the file one directory above the mxCuBE v1.3 plugin working directory:
strDir = os.path.dirname(self.getWorkingDirectory())
strPath = os.path.join(strDir, "bestfile.par")
EDUtilsFile.writeFile(strPath, strBestfilePar)
break
# Execute plugin which creates a simple HTML page
self.executeSimpleHTML(xsDataResultCharacterisation)
# Upload the best wilson plot path to ISPyB
strBestWilsonPlotPath = EDHandlerXSDataISPyBv1_4.getBestWilsonPlotPath(
xsDataResultCharacterisation)
if strBestWilsonPlotPath is not None and strPyArchPathToDNAFileDirectory is not None:
# Copy wilson path to Pyarch
strBestWilsonPlotPyarchPath = os.path.join(
strPyArchPathToDNAFileDirectory,
os.path.basename(strBestWilsonPlotPath))
if not os.path.exists(strBestWilsonPlotPyarchPath):
if not os.path.exists(
os.path.dirname(strBestWilsonPlotPyarchPath)):
os.makedirs(
os.path.dirname(strBestWilsonPlotPyarchPath), 755)
shutil.copy(strBestWilsonPlotPath,
strBestWilsonPlotPyarchPath)
self.DEBUG("Best wilson pyarch path: %s " %
strBestWilsonPlotPyarchPath)
if self.edPluginControlInterface.dataOutput.resultControlISPyB is not None:
xsDataInputISPyBSetBestWilsonPlotPath = XSDataInputISPyBSetBestWilsonPlotPath(
)
xsDataInputISPyBSetBestWilsonPlotPath.dataCollectionId = self.edPluginControlInterface.dataOutput.resultControlISPyB.dataCollectionId
xsDataInputISPyBSetBestWilsonPlotPath.bestWilsonPlotPath = XSDataString(
strBestWilsonPlotPyarchPath)
edPluginSetBestWilsonPlotPath = self.loadPlugin(
"EDPluginISPyBSetBestWilsonPlotPathv1_4",
"ISPyBSetBestWilsonPlotPath")
edPluginSetBestWilsonPlotPath.dataInput = xsDataInputISPyBSetBestWilsonPlotPath
edPluginSetBestWilsonPlotPath.executeSynchronous()
def storeResultsInISPyB(self, _strSubject, _strMessage):
strSubject = _strSubject
strMessage = _strMessage
xsDataResultCharacterisation = self.edPluginControlInterface.getDataOutput().getResultCharacterisation()
if self.bIsEigerDetector:
xsDataResultCharacterisation = self.makeNumberOfImagesMultipleOf100(xsDataResultCharacterisation)
self.xsDataResultMXCuBE.setCharacterisationResult(xsDataResultCharacterisation)
xsDataResultControlISPyB = self.edPluginControlInterface.getDataOutput().getResultControlISPyB()
if xsDataResultControlISPyB != None:
self.xsDataResultMXCuBE.setScreeningId(xsDataResultControlISPyB.getScreeningId())
if xsDataResultCharacterisation != None:
self.xsDataResultMXCuBE.characterisationResult = xsDataResultCharacterisation
strPathCharacterisationResult = os.path.join(self.getWorkingDirectory(), "CharacterisationResult.xml")
xsDataResultCharacterisation.exportToFile(strPathCharacterisationResult)
self.xsDataResultMXCuBE.setListOfOutputFiles(XSDataString(strPathCharacterisationResult))
# For the moment, create "DNA" style output directory
strPathToDNAFileDirectory = self.createDNAFileDirectoryPath(xsDataResultCharacterisation)
xsDataDictionaryLogFile = None
if self.createDNAFileDirectory(strPathToDNAFileDirectory):
xsDataDictionaryLogFile = self.createOutputFileDictionary(
xsDataResultCharacterisation, strPathToDNAFileDirectory
)
strPyArchPathToDNAFileDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(strPathToDNAFileDirectory)
if self.createDNAFileDirectory(strPyArchPathToDNAFileDirectory):
xsDataDictionaryLogFile = self.createOutputFileDictionary(
xsDataResultCharacterisation, strPyArchPathToDNAFileDirectory
)
self.xsDataResultMXCuBE.setOutputFileDictionary(xsDataDictionaryLogFile)
if xsDataResultCharacterisation.getStatusMessage():
strMessage += "\n\n"
strMessage += xsDataResultCharacterisation.getStatusMessage().getValue()
if xsDataResultCharacterisation.getShortSummary():
strMessage += "\n\n"
strMessage += xsDataResultCharacterisation.getShortSummary().getValue()
self.sendEmail(strSubject, strMessage)
# Fix for bug EDNA-55 : If burning strategy EDNA2html shouldn't be run
bRunExecOutputHTML = False
xsDataInputMXCuBE = self.getDataInput()
xsDataDiffractionPlan = xsDataInputMXCuBE.getDiffractionPlan()
if xsDataDiffractionPlan is not None and xsDataDiffractionPlan.getStrategyOption() is not None:
strStrategyOption = xsDataDiffractionPlan.getStrategyOption().getValue()
if strStrategyOption.find("-DamPar") != -1:
bRunExecOutputHTML = False
if (self.edPluginExecOutputHTML is not None) and bRunExecOutputHTML:
self.edPluginExecOutputHTML.setDataInput(
XSDataFile(XSDataString(strPathToDNAFileDirectory)), "dnaFileDirectory"
)
self.edPluginExecOutputHTML.execute()
# Fix for bug MXSUP-251: Put the BEST .par file in the EDNA characterisation root directory
xsDataIntegrationResult = xsDataResultCharacterisation.getIntegrationResult()
if xsDataIntegrationResult:
listXSDataIntegrationSubWedgeResult = xsDataIntegrationResult.getIntegrationSubWedgeResult()
for xsDataIntegrationSubWedgeResult in listXSDataIntegrationSubWedgeResult:
if xsDataIntegrationSubWedgeResult.getBestfilePar() is not None:
strBestfilePar = xsDataIntegrationSubWedgeResult.getBestfilePar().getValue()
# Put the file one directory above the mxCuBE v1.3 plugin working directory:
strDir = os.path.dirname(self.getWorkingDirectory())
strPath = os.path.join(strDir, "bestfile.par")
EDUtilsFile.writeFile(strPath, strBestfilePar)
break
# Execute plugin which creates a simple HTML page
self.executeSimpleHTML(xsDataResultCharacterisation)
# Upload the best wilson plot path to ISPyB
strBestWilsonPlotPath = EDHandlerXSDataISPyBv1_4.getBestWilsonPlotPath(xsDataResultCharacterisation)
strBestWilsonPlotPyarchPath = None
if strBestWilsonPlotPath is not None and strPyArchPathToDNAFileDirectory is not None:
# Copy wilson path to Pyarch
strBestWilsonPlotPyarchPath = os.path.join(
strPyArchPathToDNAFileDirectory, os.path.basename(strBestWilsonPlotPath)
)
if not os.path.exists(strBestWilsonPlotPyarchPath):
if not os.path.exists(os.path.dirname(strBestWilsonPlotPyarchPath)):
os.makedirs(os.path.dirname(strBestWilsonPlotPyarchPath), 755)
shutil.copy(strBestWilsonPlotPath, strBestWilsonPlotPyarchPath)
self.DEBUG("Best wilson pyarch path: %s " % strBestWilsonPlotPyarchPath)
if self.edPluginControlInterface.dataOutput.resultControlISPyB is not None:
xsDataInputISPyBSetBestWilsonPlotPath = XSDataInputISPyBSetBestWilsonPlotPath()
xsDataInputISPyBSetBestWilsonPlotPath.dataCollectionId = (
self.edPluginControlInterface.dataOutput.resultControlISPyB.dataCollectionId
)
xsDataInputISPyBSetBestWilsonPlotPath.bestWilsonPlotPath = XSDataString(strBestWilsonPlotPyarchPath)
edPluginSetBestWilsonPlotPath = self.loadPlugin(
"EDPluginISPyBSetBestWilsonPlotPathv1_4", "ISPyBSetBestWilsonPlotPath"
)
edPluginSetBestWilsonPlotPath.dataInput = xsDataInputISPyBSetBestWilsonPlotPath
edPluginSetBestWilsonPlotPath.executeSynchronous()
# Only for the ESRF:
if EDUtilsPath.isESRF():
# For EXI: create workflow entry with one workflow step
self.edPluginStoreWorkflow = self.loadPlugin(self.strPluginStoreWorkflow)
self.edPluginStoreWorkflowStep = self.loadPlugin(self.strPluginStoreWorkflowStep)
self.edPluginUpdateDataCollectionGroupWorkflowId = self.loadPlugin(
self.strUpdateDataCollectionGroupWorkflowId
)
xsDataISPyBWorkflow = XSDataISPyBWorkflow()
xsDataISPyBWorkflow.workflowType = XSDataString("Characterisation")
xsDataISPyBWorkflow.workflowTitle = XSDataString("Characterisation")
xsDataInputISPyBStoreWorkflow = XSDataInputISPyBStoreWorkflow()
xsDataInputISPyBStoreWorkflow.workflow = xsDataISPyBWorkflow
self.edPluginStoreWorkflow.dataInput = xsDataInputISPyBStoreWorkflow
self.edPluginStoreWorkflow.executeSynchronous()
if (
self.edPluginStoreWorkflow.dataOutput is not None
and self.edPluginStoreWorkflow.dataOutput.workflowId is not None
):
workflowId = self.edPluginStoreWorkflow.dataOutput.workflowId.value
# Update data collection group
xsDataInputISPyBUpdateDataCollectionGroupWorkflowId = (
XSDataInputISPyBUpdateDataCollectionGroupWorkflowId()
)
xsDataInputISPyBUpdateDataCollectionGroupWorkflowId.workflowId = XSDataInteger(workflowId)
xsDataInputISPyBUpdateDataCollectionGroupWorkflowId.fileLocation = XSDataString(
os.path.dirname(self.xsDataFirstImage.path.value)
)
xsDataInputISPyBUpdateDataCollectionGroupWorkflowId.fileName = XSDataString(
os.path.basename(self.xsDataFirstImage.path.value)
)
self.edPluginUpdateDataCollectionGroupWorkflowId.dataInput = (
xsDataInputISPyBUpdateDataCollectionGroupWorkflowId
)
self.edPluginUpdateDataCollectionGroupWorkflowId.executeSynchronous()
xsDataInputISPyBStoreWorkflowStep = XSDataInputISPyBStoreWorkflowStep()
xsDataInputISPyBStoreWorkflowStep.workflowId = XSDataInteger(workflowId)
xsDataInputISPyBStoreWorkflowStep.workflowStepType = XSDataString("Characterisation")
xsDataInputISPyBStoreWorkflowStep.status = XSDataString("Success")
if strBestWilsonPlotPyarchPath is not None:
xsDataInputISPyBStoreWorkflowStep.imageResultFilePath = XSDataString(
strBestWilsonPlotPyarchPath
)
xsDataInputISPyBStoreWorkflowStep.htmlResultFilePath = XSDataString(strPyArchPathToDNAFileDirectory)
if self.edPluginExecSimpleHTML.dataOutput is not None:
strResultFilePath = self.edPluginExecSimpleHTML.dataOutput.pathToJsonFile.path.value
# strPyarchResultFilePath = EDHandlerESRFPyarchv1_0.createPyarchFilePath(strResultFilePath)
xsDataInputISPyBStoreWorkflowStep.resultFilePath = XSDataString(strResultFilePath)
self.edPluginStoreWorkflowStep.dataInput = xsDataInputISPyBStoreWorkflowStep
self.edPluginStoreWorkflowStep.executeSynchronous()
def storeResultsInISPyB(self, _strSubject, _strMessage):
strSubject = _strSubject
strMessage = _strMessage
xsDataResultCharacterisation = self.edPluginControlInterface.getDataOutput().getResultCharacterisation()
self.xsDataResultMXCuBE.setCharacterisationResult(xsDataResultCharacterisation)
xsDataResultControlISPyB = self.edPluginControlInterface.getDataOutput().getResultControlISPyB()
if xsDataResultControlISPyB != None:
self.xsDataResultMXCuBE.setScreeningId(xsDataResultControlISPyB.getScreeningId())
if xsDataResultCharacterisation != None:
self.xsDataResultMXCuBE.characterisationResult = xsDataResultCharacterisation
strPathCharacterisationResult = os.path.join(self.getWorkingDirectory(), "CharacterisationResult.xml")
xsDataResultCharacterisation.exportToFile(strPathCharacterisationResult)
self.xsDataResultMXCuBE.setListOfOutputFiles(XSDataString(strPathCharacterisationResult))
# For the moment, create "DNA" style output directory
strPathToDNAFileDirectory = self.createDNAFileDirectoryPath(xsDataResultCharacterisation)
xsDataDictionaryLogFile = None
if (self.createDNAFileDirectory(strPathToDNAFileDirectory)):
xsDataDictionaryLogFile = self.createOutputFileDictionary(xsDataResultCharacterisation, strPathToDNAFileDirectory)
strPyArchPathToDNAFileDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(strPathToDNAFileDirectory)
if (self.createDNAFileDirectory(strPyArchPathToDNAFileDirectory)):
xsDataDictionaryLogFile = self.createOutputFileDictionary(xsDataResultCharacterisation, strPyArchPathToDNAFileDirectory)
self.xsDataResultMXCuBE.setOutputFileDictionary(xsDataDictionaryLogFile)
if xsDataResultCharacterisation.getStatusMessage():
strMessage += "\n\n"
strMessage += xsDataResultCharacterisation.getStatusMessage().getValue()
if xsDataResultCharacterisation.getShortSummary():
strMessage += "\n\n"
strMessage += xsDataResultCharacterisation.getShortSummary().getValue()
self.sendEmail(strSubject, strMessage)
# Fix for bug EDNA-55 : If burning strategy EDNA2html shouldn't be run
bRunExecOutputHTML = False
xsDataInputMXCuBE = self.getDataInput()
xsDataDiffractionPlan = xsDataInputMXCuBE.getDiffractionPlan()
if xsDataDiffractionPlan.getStrategyOption() is not None:
strStrategyOption = xsDataDiffractionPlan.getStrategyOption().getValue()
if strStrategyOption.find("-DamPar") != -1:
bRunExecOutputHTML = False
if (self.edPluginExecOutputHTML is not None) and bRunExecOutputHTML:
self.edPluginExecOutputHTML.setDataInput(XSDataFile(XSDataString(strPathToDNAFileDirectory)), "dnaFileDirectory")
self.edPluginExecOutputHTML.execute()
# Fix for bug MXSUP-251: Put the BEST .par file in the EDNA characterisation root directory
xsDataIntegrationResult = xsDataResultCharacterisation.getIntegrationResult()
if xsDataIntegrationResult:
listXSDataIntegrationSubWedgeResult = xsDataIntegrationResult.getIntegrationSubWedgeResult()
for xsDataIntegrationSubWedgeResult in listXSDataIntegrationSubWedgeResult:
if xsDataIntegrationSubWedgeResult.getBestfilePar() is not None:
strBestfilePar = xsDataIntegrationSubWedgeResult.getBestfilePar().getValue()
# Put the file one directory above the mxCuBE v1.3 plugin working directory:
strDir = os.path.dirname(self.getWorkingDirectory())
strPath = os.path.join(strDir, "bestfile.par")
EDUtilsFile.writeFile(strPath, strBestfilePar)
break
# Execute plugin which creates a simple HTML page
self.executeSimpleHTML(xsDataResultCharacterisation)
# Upload the best wilson plot path to ISPyB
strBestWilsonPlotPath = EDHandlerXSDataISPyBv1_4.getBestWilsonPlotPath(xsDataResultCharacterisation)
if strBestWilsonPlotPath is not None and strPyArchPathToDNAFileDirectory is not None:
# Copy wilson path to Pyarch
strBestWilsonPlotPyarchPath = os.path.join(strPyArchPathToDNAFileDirectory, os.path.basename(strBestWilsonPlotPath))
if not os.path.exists(strBestWilsonPlotPyarchPath):
if not os.path.exists(os.path.dirname(strBestWilsonPlotPyarchPath)):
os.makedirs(os.path.dirname(strBestWilsonPlotPyarchPath), 755)
shutil.copy(strBestWilsonPlotPath, strBestWilsonPlotPyarchPath)
self.DEBUG("Best wilson pyarch path: %s " % strBestWilsonPlotPyarchPath)
if self.edPluginControlInterface.dataOutput.resultControlISPyB is not None:
xsDataInputISPyBSetBestWilsonPlotPath = XSDataInputISPyBSetBestWilsonPlotPath()
xsDataInputISPyBSetBestWilsonPlotPath.dataCollectionId = self.edPluginControlInterface.dataOutput.resultControlISPyB.dataCollectionId
xsDataInputISPyBSetBestWilsonPlotPath.bestWilsonPlotPath = XSDataString(strBestWilsonPlotPyarchPath)
edPluginSetBestWilsonPlotPath = self.loadPlugin("EDPluginISPyBSetBestWilsonPlotPathv1_4", "ISPyBSetBestWilsonPlotPath")
edPluginSetBestWilsonPlotPath.dataInput = xsDataInputISPyBSetBestWilsonPlotPath
edPluginSetBestWilsonPlotPath.executeSynchronous()
