def process(self, _edObject=None):
"""
Stores the contents of the AutoProcContainer in ISPyB.
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreScreeningv1_4.process")
xsDataInputISPyBStoreScreening = self.getDataInput()
httpAuthenticatedToolsForAutoprocessingWebService1 = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForBLSampleWebServiceWsdl = Client(
self.strToolsForBLSampleWebServiceWsdl,
transport=httpAuthenticatedToolsForAutoprocessingWebService1)
httpAuthenticatedToolsForAutoprocessingWebService2 = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForScreeningEDNAWebServiceWsdl = Client(
self.strToolsForScreeningEDNAWebServiceWsdl,
transport=httpAuthenticatedToolsForAutoprocessingWebService2)
self.bContinue = True
# DiffractionPlan
xsDataISPyBDiffractionPlan = xsDataInputISPyBStoreScreening.diffractionPlan
iDiffractionPlanId = self.storeOrUpdateDiffractionPlan(
clientToolsForBLSampleWebServiceWsdl, xsDataISPyBDiffractionPlan)
if iDiffractionPlanId is None:
self.ERROR("Couldn't create entry for diffraction plan in ISPyB!")
self.setFailure()
self.bContinue = False
# Screening
xsDataISPyBScreening = xsDataInputISPyBStoreScreening.screening
self.iScreeningId = self.storeOrUpdateScreening(
clientToolsForScreeningEDNAWebServiceWsdl, xsDataISPyBScreening,
iDiffractionPlanId)
if self.iScreeningId is None:
self.ERROR("Couldn't create entry for screening in ISPyB!")
self.setFailure()
self.bContinue = False
# Screening Output Container
for xsDataISPyBScreeningOutputContainer in xsDataInputISPyBStoreScreening.screeningOutputContainer:
xsDataISPyBScreeningOutput = xsDataISPyBScreeningOutputContainer.screeningOutput
iScreeningOutputId = self.storeOrUpdateScreeningOutput(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningOutput, self.iScreeningId)
if iScreeningOutputId is None:
self.ERROR("Couldn't create entry for screening in ISPyB!")
self.setFailure()
self.bContinue = False
for xsDataISPyBScreeningOutputLattice in xsDataISPyBScreeningOutputContainer.screeningOutputLattice:
iScreeningOutputLatticeId = self.storeOrUpdateScreeningOutputLattice(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningOutputLattice, iScreeningOutputId)
if iScreeningOutputLatticeId is None:
self.ERROR(
"Couldn't create entry for screening lattice in ISPyB!"
)
self.setFailure()
self.bContinue = False
for xsDataISPyBScreeningStrategyContainer in xsDataISPyBScreeningOutputContainer.screeningStrategyContainer:
# Create an empty object of type XSDataISPyBScreeningStrategy
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
iScreeningStrategyId = self.storeOrUpdateScreeningStrategy(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningStrategy, iScreeningOutputId)
if iScreeningStrategyId is None:
self.ERROR(
"Couldn't create entry for screening strategy in ISPyB!"
)
self.setFailure()
self.bContinue = False
for xsDataISPyBScreeningStrategyWedgeContainer in xsDataISPyBScreeningStrategyContainer.screeningStrategyWedgeContainer:
xsDataISPyBScreeningStrategyWedge = xsDataISPyBScreeningStrategyWedgeContainer.screeningStrategyWedge
iScreeningStrategyWedgeId = self.storeOrUpdateScreeningStrategyWedge(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningStrategyWedge,
iScreeningStrategyId)
if iScreeningStrategyWedgeId is None:
self.ERROR(
"Couldn't create entry for screening strategy in ISPyB!"
)
self.setFailure()
self.bContinue = False
for xsDataISPyBScreeningStrategySubWedge in xsDataISPyBScreeningStrategyWedgeContainer.screeningStrategySubWedge:
iScreeningStrategySubWedgeId = self.storeOrUpdateScreeningStrategySubWedge(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningStrategySubWedge,
iScreeningStrategyWedgeId)
if iScreeningStrategySubWedgeId is None:
self.ERROR(
"Couldn't create entry for screening strategy in ISPyB!"
)
self.setFailure()
self.bContinue = False
def generateLegacyXSDataISPyBStrategy(_xsDataResultCharacterisation, _xsDataISPyBScreeningOutputContainer):
# Anomalus data
bAnomalousData = False
xsDataCollection = _xsDataResultCharacterisation.dataCollection
if xsDataCollection is not None:
xsDataDiffractionPlan = xsDataCollection.diffractionPlan
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.anomalousData is not None:
bAnomalousData = xsDataDiffractionPlan.getAnomalousData().getValue()
# Use the existing xsDataISPyBScreeningStrategy in the _xsDataISPyBScreeningOutputContainer for the first sub wedge:
if len(_xsDataISPyBScreeningOutputContainer.screeningStrategyContainer) > 0:
xsDataISPyBScreeningStrategyContainerFirst = _xsDataISPyBScreeningOutputContainer.screeningStrategyContainer[0]
xsDataISPyBScreeningStrategyFirst = xsDataISPyBScreeningStrategyContainerFirst.screeningStrategy
# Strategy information
bFirstStrategy = True
xsDataResultStrategy = _xsDataResultCharacterisation.getStrategyResult()
if (xsDataResultStrategy is not None):
pyListXSDataCollectionPlan = xsDataResultStrategy.getCollectionPlan()
if (pyListXSDataCollectionPlan is not None):
for xsDataCollectionPlan in pyListXSDataCollectionPlan:
iCollectionPlanNumber = xsDataCollectionPlan.getCollectionPlanNumber().getValue()
pyStrCollectionPlanComment = None
if (xsDataCollectionPlan.getComment() is not None):
pyStrCollectionPlanComment = xsDataCollectionPlan.getComment().getValue()
fCompleteness = None
fMultiplicity = None
fResolution = None
fRankingResolution = None
fTransmission = None
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
if (xsDataStrategySummary is not None):
if (xsDataStrategySummary.getCompleteness() is not None):
fCompleteness = xsDataStrategySummary.getCompleteness().getValue()
if (xsDataStrategySummary.getRedundancy() is not None):
fMultiplicity = xsDataStrategySummary.getRedundancy().getValue()
if (xsDataStrategySummary.getResolution() is not None):
fResolution = xsDataStrategySummary.getResolution().getValue()
if (xsDataStrategySummary.getRankingResolution() is not None):
fRankingResolution = xsDataStrategySummary.getRankingResolution().getValue()
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
if (xsDataCollectionStrategy is not None):
pyListXSDataSubWedge = xsDataCollectionStrategy.getSubWedge()
if (pyListXSDataSubWedge is not None):
for xsDataSubWedge in pyListXSDataSubWedge:
iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber().getValue()
if bFirstStrategy:
xsDataISPyBScreeningStrategy = xsDataISPyBScreeningStrategyFirst
else:
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
xsDataISPyBScreeningStrategyContainer = XSDataISPyBScreeningStrategyContainer()
xsDataISPyBScreeningStrategyContainer.screeningStrategy = xsDataISPyBScreeningStrategy
fPhiStart = xsDataSubWedge.getExperimentalCondition().getGoniostat().getRotationAxisStart().getValue()
fPhiEnd = xsDataSubWedge.getExperimentalCondition().getGoniostat().getRotationAxisEnd().getValue()
fRotation = xsDataSubWedge.getExperimentalCondition().getGoniostat().getOscillationWidth().getValue()
fExposureTime = xsDataSubWedge.getExperimentalCondition().getBeam().getExposureTime().getValue()
fTransmission = None
if xsDataSubWedge.experimentalCondition.beam.transmission:
fTransmission = xsDataSubWedge.experimentalCondition.beam.transmission.value
pyStrProgram = "BEST: Wedge no %d," % iCollectionPlanNumber
if (pyStrCollectionPlanComment is not None):
pyStrProgram += " ( %s )" % pyStrCollectionPlanComment
pyStrProgram += " sub wedge no %d" % iSubWedgeNumber
xsDataISPyBScreeningStrategy.setPhiStart(XSDataDouble(fPhiStart))
xsDataISPyBScreeningStrategy.setPhiEnd(XSDataDouble(fPhiEnd))
xsDataISPyBScreeningStrategy.setRotation(XSDataDouble(fRotation))
xsDataISPyBScreeningStrategy.setExposureTime(XSDataDouble(fExposureTime))
if fTransmission is not None:
xsDataISPyBScreeningStrategy.transmission = XSDataDouble(fTransmission)
if (fCompleteness is not None):
xsDataISPyBScreeningStrategy.setCompleteness(XSDataDouble(fCompleteness))
if (fMultiplicity is not None):
xsDataISPyBScreeningStrategy.setMultiplicity(XSDataDouble(fMultiplicity))
if (fResolution is not None):
xsDataISPyBScreeningStrategy.setResolution(XSDataDouble(fResolution))
if (fRankingResolution is not None):
xsDataISPyBScreeningStrategy.setRankingResolution(XSDataDouble(fRankingResolution))
if (bAnomalousData is not None):
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(bAnomalousData))
else:
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(False))
xsDataISPyBScreeningStrategy.setProgram(XSDataString(pyStrProgram))
if bFirstStrategy:
bFirstStrategy = False
else:
_xsDataISPyBScreeningOutputContainer.addScreeningStrategyContainer(xsDataISPyBScreeningStrategyContainer)
def generateXSDataISPyBScreeningOutputContainer(_xsDataResultCharacterisation, _strStatusMessage):
xsDataISPyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutputLattice = None
# Indexing information
bSuccessfulIndexing = False
xsDataIndexingResult = _xsDataResultCharacterisation.getIndexingResult()
if xsDataIndexingResult is not None:
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution()
if xsDataIndexingSolutionSelected is not None:
xsDataISPyBScreeningOutputLattice = XSDataISPyBScreeningOutputLattice()
bSuccessfulIndexing = True
xsDataStatisticsIndexing = xsDataIndexingSolutionSelected.getStatistics()
if xsDataStatisticsIndexing is not None:
xsDataISPyBScreeningOutput.beamShiftX = xsDataStatisticsIndexing.beamPositionShiftX
xsDataISPyBScreeningOutput.beamShiftY = xsDataStatisticsIndexing.beamPositionShiftY
xsDataISPyBScreeningOutput.spotDeviationR = xsDataStatisticsIndexing.spotDeviationPositional
xsDataISPyBScreeningOutput.spotDeviationTheta = xsDataStatisticsIndexing.spotDeviationAngular
if (xsDataStatisticsIndexing.spotsTotal is not None) and (
xsDataStatisticsIndexing.spotsUsed is not None
):
iSpotsTotal = xsDataStatisticsIndexing.spotsTotal.value
iSpotsUsed = xsDataStatisticsIndexing.spotsUsed.value
xsDataISPyBScreeningOutput.numSpotsFound = xsDataStatisticsIndexing.spotsTotal
xsDataISPyBScreeningOutput.numSpotsUsed = xsDataStatisticsIndexing.spotsUsed
xsDataISPyBScreeningOutput.numSpotsRejected = XSDataInteger(iSpotsTotal - iSpotsUsed)
xsDataCrystal = xsDataIndexingSolutionSelected.crystal
xsDataISPyBScreeningOutput.mosaicityEstimated = XSDataBoolean(False)
if xsDataCrystal is not None:
if xsDataCrystal.mosaicity is not None:
xsDataISPyBScreeningOutput.mosaicity = xsDataCrystal.mosaicity
xsDataISPyBScreeningOutput.mosaicityEstimated = XSDataBoolean(True)
xsDataCell = xsDataCrystal.cell
if xsDataCell is not None:
xsDataISPyBScreeningOutputLattice.unitCell_a = xsDataCell.length_a
xsDataISPyBScreeningOutputLattice.unitCell_b = xsDataCell.length_b
xsDataISPyBScreeningOutputLattice.unitCell_c = xsDataCell.length_c
xsDataISPyBScreeningOutputLattice.unitCell_alpha = xsDataCell.angle_alpha
xsDataISPyBScreeningOutputLattice.unitCell_beta = xsDataCell.angle_beta
xsDataISPyBScreeningOutputLattice.unitCell_gamma = xsDataCell.angle_gamma
xsDataSpaceGroup = xsDataCrystal.spaceGroup
if xsDataSpaceGroup is not None:
xsDataISPyBScreeningOutputLattice.spaceGroup = xsDataSpaceGroup.name
if bSuccessfulIndexing:
xsDataISPyBScreeningOutput.setIndexingSuccess(XSDataBoolean(True))
if _strStatusMessage:
xsDataISPyBScreeningOutput.setStatusDescription(XSDataString(_strStatusMessage))
else:
xsDataISPyBScreeningOutput.setStatusDescription(XSDataString("Indexing successful"))
else:
xsDataISPyBScreeningOutput.setIndexingSuccess(XSDataBoolean(False))
if _strStatusMessage:
xsDataISPyBScreeningOutput.setStatusDescription(XSDataString(_strStatusMessage))
else:
xsDataISPyBScreeningOutput.setStatusDescription(XSDataString("Indexing failed"))
# Strategy information
xsDataResultStrategy = _xsDataResultCharacterisation.strategyResult
xsDataISPyBScreeningStrategyContainer = None
xsDataISPyBScreeningStrategyWedgeContainer = None
if xsDataResultStrategy is None:
xsDataISPyBScreeningOutput.setStrategySuccess(XSDataBoolean(False))
else:
xsDataISPyBScreeningOutput.setStrategySuccess(XSDataBoolean(True))
xsDataISPyBScreeningStrategyContainer = XSDataISPyBScreeningStrategyContainer()
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
listXSDataCollectionPlan = xsDataResultStrategy.collectionPlan
for xsDataCollectionPlan in listXSDataCollectionPlan:
numberOfImagesWedge = None
xsDataISPyBScreeningStrategyWedge = XSDataISPyBScreeningStrategyWedge()
xsDataISPyBScreeningStrategyWedgeContainer = XSDataISPyBScreeningStrategyWedgeContainer()
xsDataISPyBScreeningStrategyWedge.wedgeNumber = xsDataCollectionPlan.collectionPlanNumber
strCollectionPlanComment = None
if xsDataCollectionPlan.getComment() is not None:
strCollectionPlanComment = xsDataCollectionPlan.getComment().getValue()
xsDataStrategySummary = xsDataCollectionPlan.strategySummary
if xsDataStrategySummary is not None:
xsDataISPyBScreeningStrategyWedge.completeness = xsDataStrategySummary.completeness
xsDataISPyBScreeningStrategyWedge.resolution = xsDataStrategySummary.resolution
xsDataISPyBScreeningStrategyWedge.multiplicity = xsDataStrategySummary.redundancy
xsDataISPyBScreeningStrategy.rankingResolution = xsDataStrategySummary.rankingResolution
xsDataCollectionStrategy = xsDataCollectionPlan.collectionStrategy
if xsDataCollectionStrategy is not None:
for xsDataSubWedge in xsDataCollectionStrategy.subWedge:
numberOfImagesSubWedge = None
xsDataISPyBScreeningStrategySubWedge = XSDataISPyBScreeningStrategySubWedge()
xsDataISPyBScreeningStrategySubWedge.subWedgeNumber = xsDataSubWedge.subWedgeNumber
xsDataISPyBScreeningStrategySubWedge.axisStart = (
xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart
)
xsDataISPyBScreeningStrategySubWedge.axisEnd = (
xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd
)
xsDataISPyBScreeningStrategySubWedge.oscillationRange = (
xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth
)
# Number of images
if (
(xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart is not None)
and (xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd is not None)
and (xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth is not None)
):
numberOfImagesSubWedge = int(
(
xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd.value
- xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart.value
)
/ xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth.value
+ 0.5
)
xsDataISPyBScreeningStrategySubWedge.numberOfImages = XSDataInteger(numberOfImagesSubWedge)
if numberOfImagesWedge is None:
numberOfImagesWedge = numberOfImagesSubWedge
else:
numberOfImagesWedge += numberOfImagesSubWedge
xsDataISPyBScreeningStrategySubWedge.exposureTime = (
xsDataSubWedge.experimentalCondition.beam.exposureTime
)
xsDataISPyBScreeningStrategySubWedge.transmission = (
xsDataSubWedge.experimentalCondition.beam.transmission
)
xsDataISPyBScreeningStrategyWedgeContainer.addScreeningStrategySubWedge(
xsDataISPyBScreeningStrategySubWedge
)
if numberOfImagesWedge is not None:
xsDataISPyBScreeningStrategyWedge.numberOfImages = XSDataInteger(numberOfImagesWedge)
xsDataISPyBScreeningStrategyWedgeContainer.screeningStrategyWedge = xsDataISPyBScreeningStrategyWedge
xsDataISPyBScreeningStrategyContainer.addScreeningStrategyWedgeContainer(
xsDataISPyBScreeningStrategyWedgeContainer
)
xsDataISPyBScreeningStrategyContainer.screeningStrategy = xsDataISPyBScreeningStrategy
# Assembly
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer()
xsDataISPyBScreeningOutputContainer.screeningOutput = xsDataISPyBScreeningOutput
if xsDataISPyBScreeningOutputLattice is not None:
xsDataISPyBScreeningOutputContainer.addScreeningOutputLattice(xsDataISPyBScreeningOutputLattice)
if xsDataISPyBScreeningStrategyContainer is not None:
xsDataISPyBScreeningOutputContainer.addScreeningStrategyContainer(xsDataISPyBScreeningStrategyContainer)
return xsDataISPyBScreeningOutputContainer
def generateLegacyXSDataISPyBStrategy(
_xsDataResultCharacterisation,
_xsDataISPyBScreeningOutputContainer):
# Anomalus data
bAnomalousData = False
xsDataCollection = _xsDataResultCharacterisation.dataCollection
if xsDataCollection is not None:
xsDataDiffractionPlan = xsDataCollection.diffractionPlan
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.anomalousData is not None:
bAnomalousData = xsDataDiffractionPlan.getAnomalousData(
).getValue()
# Use the existing xsDataISPyBScreeningStrategy in the _xsDataISPyBScreeningOutputContainer for the first sub wedge:
if len(_xsDataISPyBScreeningOutputContainer.screeningStrategyContainer
) > 0:
xsDataISPyBScreeningStrategyContainerFirst = _xsDataISPyBScreeningOutputContainer.screeningStrategyContainer[
0]
xsDataISPyBScreeningStrategyFirst = xsDataISPyBScreeningStrategyContainerFirst.screeningStrategy
# Strategy information
bFirstStrategy = True
xsDataResultStrategy = _xsDataResultCharacterisation.getStrategyResult(
)
if (xsDataResultStrategy is not None):
pyListXSDataCollectionPlan = xsDataResultStrategy.getCollectionPlan(
)
if (pyListXSDataCollectionPlan is not None):
for xsDataCollectionPlan in pyListXSDataCollectionPlan:
iCollectionPlanNumber = xsDataCollectionPlan.getCollectionPlanNumber(
).getValue()
pyStrCollectionPlanComment = None
if (xsDataCollectionPlan.getComment() is not None):
pyStrCollectionPlanComment = xsDataCollectionPlan.getComment(
).getValue()
fCompleteness = None
fMultiplicity = None
fResolution = None
fRankingResolution = None
fTransmission = None
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary(
)
if (xsDataStrategySummary is not None):
if (xsDataStrategySummary.getCompleteness()
is not None):
fCompleteness = xsDataStrategySummary.getCompleteness(
).getValue()
if (xsDataStrategySummary.getRedundancy()
is not None):
fMultiplicity = xsDataStrategySummary.getRedundancy(
).getValue()
if (xsDataStrategySummary.getResolution()
is not None):
fResolution = xsDataStrategySummary.getResolution(
).getValue()
if (xsDataStrategySummary.getRankingResolution()
is not None):
fRankingResolution = xsDataStrategySummary.getRankingResolution(
).getValue()
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy(
)
if (xsDataCollectionStrategy is not None):
pyListXSDataSubWedge = xsDataCollectionStrategy.getSubWedge(
)
if (pyListXSDataSubWedge is not None):
for xsDataSubWedge in pyListXSDataSubWedge:
iSubWedgeNumber = xsDataSubWedge.getSubWedgeNumber(
).getValue()
if bFirstStrategy:
xsDataISPyBScreeningStrategy = xsDataISPyBScreeningStrategyFirst
else:
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy(
)
xsDataISPyBScreeningStrategyContainer = XSDataISPyBScreeningStrategyContainer(
)
xsDataISPyBScreeningStrategyContainer.screeningStrategy = xsDataISPyBScreeningStrategy
fPhiStart = xsDataSubWedge.getExperimentalCondition(
).getGoniostat().getRotationAxisStart(
).getValue()
fPhiEnd = xsDataSubWedge.getExperimentalCondition(
).getGoniostat().getRotationAxisEnd(
).getValue()
fRotation = xsDataSubWedge.getExperimentalCondition(
).getGoniostat().getOscillationWidth(
).getValue()
fExposureTime = xsDataSubWedge.getExperimentalCondition(
).getBeam().getExposureTime().getValue()
fTransmission = None
if xsDataSubWedge.experimentalCondition.beam.transmission:
fTransmission = xsDataSubWedge.experimentalCondition.beam.transmission.value
pyStrProgram = "BEST: Wedge no %d," % iCollectionPlanNumber
if (pyStrCollectionPlanComment
is not None):
pyStrProgram += " ( %s )" % pyStrCollectionPlanComment
pyStrProgram += " sub wedge no %d" % iSubWedgeNumber
xsDataISPyBScreeningStrategy.setPhiStart(
XSDataDouble(fPhiStart))
xsDataISPyBScreeningStrategy.setPhiEnd(
XSDataDouble(fPhiEnd))
xsDataISPyBScreeningStrategy.setRotation(
XSDataDouble(fRotation))
xsDataISPyBScreeningStrategy.setExposureTime(
XSDataDouble(fExposureTime))
if fTransmission is not None:
xsDataISPyBScreeningStrategy.transmission = XSDataDouble(
fTransmission)
if (fCompleteness is not None):
xsDataISPyBScreeningStrategy.setCompleteness(
XSDataDouble(fCompleteness))
if (fMultiplicity is not None):
xsDataISPyBScreeningStrategy.setMultiplicity(
XSDataDouble(fMultiplicity))
if (fResolution is not None):
xsDataISPyBScreeningStrategy.setResolution(
XSDataDouble(fResolution))
if (fRankingResolution is not None):
xsDataISPyBScreeningStrategy.setRankingResolution(
XSDataDouble(fRankingResolution))
if (bAnomalousData is not None):
xsDataISPyBScreeningStrategy.setAnomalous(
XSDataBoolean(bAnomalousData))
else:
xsDataISPyBScreeningStrategy.setAnomalous(
XSDataBoolean(False))
xsDataISPyBScreeningStrategy.setProgram(
XSDataString(pyStrProgram))
if bFirstStrategy:
bFirstStrategy = False
else:
_xsDataISPyBScreeningOutputContainer.addScreeningStrategyContainer(
xsDataISPyBScreeningStrategyContainer
)
def generateXSDataISPyBScreeningOutputContainer(
_xsDataResultCharacterisation, _strStatusMessage, _fKappa, _fPhi):
xsDataISPyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutput.program = XSDataString("EDNA MXv1")
xsDataISPyBScreeningOutputLattice = None
# Indexing information
bSuccessfulIndexing = False
xsDataIndexingResult = _xsDataResultCharacterisation.getIndexingResult(
)
if (xsDataIndexingResult is not None):
xsDataIndexingSolutionSelected = xsDataIndexingResult.getSelectedSolution(
)
if (xsDataIndexingSolutionSelected is not None):
xsDataISPyBScreeningOutputLattice = XSDataISPyBScreeningOutputLattice(
)
bSuccessfulIndexing = True
xsDataStatisticsIndexing = xsDataIndexingSolutionSelected.getStatistics(
)
if (xsDataStatisticsIndexing is not None):
xsDataISPyBScreeningOutput.beamShiftX = xsDataStatisticsIndexing.beamPositionShiftX
xsDataISPyBScreeningOutput.beamShiftY = xsDataStatisticsIndexing.beamPositionShiftY
xsDataISPyBScreeningOutput.spotDeviationR = xsDataStatisticsIndexing.spotDeviationPositional
xsDataISPyBScreeningOutput.spotDeviationTheta = xsDataStatisticsIndexing.spotDeviationAngular
if ((xsDataStatisticsIndexing.spotsTotal is not None) and
(xsDataStatisticsIndexing.spotsUsed is not None)):
iSpotsTotal = xsDataStatisticsIndexing.spotsTotal.value
iSpotsUsed = xsDataStatisticsIndexing.spotsUsed.value
xsDataISPyBScreeningOutput.numSpotsFound = xsDataStatisticsIndexing.spotsTotal
xsDataISPyBScreeningOutput.numSpotsUsed = xsDataStatisticsIndexing.spotsUsed
xsDataISPyBScreeningOutput.numSpotsRejected = XSDataInteger(
iSpotsTotal - iSpotsUsed)
xsDataCrystal = xsDataIndexingSolutionSelected.crystal
xsDataISPyBScreeningOutput.mosaicityEstimated = XSDataBoolean(
False)
if (xsDataCrystal is not None):
if xsDataCrystal.mosaicity is not None:
xsDataISPyBScreeningOutput.mosaicity = xsDataCrystal.mosaicity
xsDataISPyBScreeningOutput.mosaicityEstimated = XSDataBoolean(
True)
xsDataCell = xsDataCrystal.cell
if xsDataCell is not None:
xsDataISPyBScreeningOutputLattice.unitCell_a = xsDataCell.length_a
xsDataISPyBScreeningOutputLattice.unitCell_b = xsDataCell.length_b
xsDataISPyBScreeningOutputLattice.unitCell_c = xsDataCell.length_c
xsDataISPyBScreeningOutputLattice.unitCell_alpha = xsDataCell.angle_alpha
xsDataISPyBScreeningOutputLattice.unitCell_beta = xsDataCell.angle_beta
xsDataISPyBScreeningOutputLattice.unitCell_gamma = xsDataCell.angle_gamma
xsDataSpaceGroup = xsDataCrystal.spaceGroup
if xsDataSpaceGroup is not None:
xsDataISPyBScreeningOutputLattice.spaceGroup = xsDataSpaceGroup.name
if (bSuccessfulIndexing):
xsDataISPyBScreeningOutput.setIndexingSuccess(XSDataBoolean(True))
if _strStatusMessage:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString(_strStatusMessage))
else:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString("Indexing successful"))
else:
xsDataISPyBScreeningOutput.setIndexingSuccess(XSDataBoolean(False))
if _strStatusMessage:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString(_strStatusMessage))
else:
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString("Indexing failed"))
# Strategy information
xsDataResultStrategy = _xsDataResultCharacterisation.strategyResult
xsDataISPyBScreeningStrategyContainer = None
xsDataISPyBScreeningStrategyWedgeContainer = None
if xsDataResultStrategy is None:
xsDataISPyBScreeningOutput.setStrategySuccess(XSDataBoolean(False))
else:
if xsDataResultStrategy.collectionPlan == []:
xsDataISPyBScreeningOutput.setStrategySuccess(
XSDataBoolean(False))
else:
xsDataISPyBScreeningOutput.setStrategySuccess(
XSDataBoolean(True))
xsDataISPyBScreeningStrategyContainer = XSDataISPyBScreeningStrategyContainer(
)
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
listXSDataCollectionPlan = xsDataResultStrategy.collectionPlan
fTotalExposureTime = 0.0
iTotalNumberOfImages = 0
fTotalRotationRange = 0.0
for xsDataCollectionPlan in listXSDataCollectionPlan:
numberOfImagesWedge = None
xsDataISPyBScreeningStrategyWedge = XSDataISPyBScreeningStrategyWedge(
)
xsDataISPyBScreeningStrategyWedgeContainer = XSDataISPyBScreeningStrategyWedgeContainer(
)
xsDataISPyBScreeningStrategyWedge.wedgeNumber = xsDataCollectionPlan.collectionPlanNumber
fWavelength = _xsDataResultCharacterisation.dataCollection.subWedge[
0].experimentalCondition.beam.wavelength.value
xsDataISPyBScreeningStrategyWedge.wavelength = XSDataDouble(
fWavelength)
if _fKappa is not None:
xsDataISPyBScreeningStrategyWedge.kappa = XSDataDouble(
_fKappa)
if _fPhi is not None:
xsDataISPyBScreeningStrategyWedge.phi = XSDataDouble(
_fPhi)
if (xsDataCollectionPlan.getComment() is not None):
strCollectionPlanComment = xsDataCollectionPlan.getComment(
).getValue()
xsDataISPyBScreeningStrategyWedge.comments = strCollectionPlanComment
xsDataStrategySummary = xsDataCollectionPlan.strategySummary
if xsDataStrategySummary is not None:
xsDataISPyBScreeningStrategyWedge.completeness = xsDataStrategySummary.completeness
xsDataISPyBScreeningStrategyWedge.resolution = xsDataStrategySummary.resolution
xsDataISPyBScreeningStrategyWedge.multiplicity = xsDataStrategySummary.redundancy
xsDataISPyBScreeningOutput.rankingResolution = xsDataStrategySummary.rankingResolution
if xsDataStrategySummary.totalExposureTime is not None:
fTotalExposureTime += xsDataStrategySummary.totalExposureTime.value
xsDataCollectionStrategy = xsDataCollectionPlan.collectionStrategy
if xsDataCollectionStrategy is not None:
for xsDataSubWedge in xsDataCollectionStrategy.subWedge:
numberOfImagesSubWedge = None
xsDataISPyBScreeningStrategySubWedge = XSDataISPyBScreeningStrategySubWedge(
)
xsDataISPyBScreeningStrategySubWedge.subWedgeNumber = xsDataSubWedge.subWedgeNumber
xsDataISPyBScreeningStrategySubWedge.axisStart = xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart
xsDataISPyBScreeningStrategySubWedge.axisEnd = xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd
xsDataISPyBScreeningStrategySubWedge.oscillationRange = xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth
# Number of images
if (xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart is not None) and \
(xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd is not None) and \
(xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth is not None):
numberOfImagesSubWedge = int((xsDataSubWedge.experimentalCondition.goniostat.rotationAxisEnd.value - \
xsDataSubWedge.experimentalCondition.goniostat.rotationAxisStart.value) / \
xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth.value + 0.5)
xsDataISPyBScreeningStrategySubWedge.numberOfImages = XSDataInteger(
numberOfImagesSubWedge)
if numberOfImagesWedge is None:
numberOfImagesWedge = numberOfImagesSubWedge
else:
numberOfImagesWedge += numberOfImagesSubWedge
fTotalRotationRange += xsDataSubWedge.experimentalCondition.goniostat.oscillationWidth.value * numberOfImagesSubWedge
xsDataISPyBScreeningStrategySubWedge.exposureTime = xsDataSubWedge.experimentalCondition.beam.exposureTime
xsDataISPyBScreeningStrategySubWedge.transmission = xsDataSubWedge.experimentalCondition.beam.transmission
xsDataISPyBScreeningStrategyWedgeContainer.addScreeningStrategySubWedge(
xsDataISPyBScreeningStrategySubWedge)
if numberOfImagesWedge is not None:
xsDataISPyBScreeningStrategyWedge.numberOfImages = XSDataInteger(
numberOfImagesWedge)
iTotalNumberOfImages += numberOfImagesWedge
xsDataISPyBScreeningStrategyWedgeContainer.screeningStrategyWedge = xsDataISPyBScreeningStrategyWedge
xsDataISPyBScreeningStrategyContainer.addScreeningStrategyWedgeContainer(
xsDataISPyBScreeningStrategyWedgeContainer)
xsDataISPyBScreeningOutput.totalExposureTime = XSDataDouble(
fTotalExposureTime)
xsDataISPyBScreeningOutput.totalNumberOfImages = XSDataInteger(
iTotalNumberOfImages)
xsDataISPyBScreeningOutput.totalRotationRange = XSDataDouble(
fTotalRotationRange)
xsDataISPyBScreeningStrategyContainer.screeningStrategy = xsDataISPyBScreeningStrategy
# Assembly
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer(
)
xsDataISPyBScreeningOutputContainer.screeningOutput = xsDataISPyBScreeningOutput
if xsDataISPyBScreeningOutputLattice is not None:
xsDataISPyBScreeningOutputContainer.addScreeningOutputLattice(
xsDataISPyBScreeningOutputLattice)
if xsDataISPyBScreeningStrategyContainer is not None:
xsDataISPyBScreeningOutputContainer.addScreeningStrategyContainer(
xsDataISPyBScreeningStrategyContainer)
return xsDataISPyBScreeningOutputContainer
def process(self, _edObject=None):
"""
Stores the contents of the AutoProcContainer in ISPyB.
"""
EDPluginISPyBv1_4.process(self)
self.DEBUG("EDPluginISPyBStoreScreeningv1_4.process")
xsDataInputISPyBStoreScreening = self.getDataInput()
httpAuthenticatedToolsForAutoprocessingWebService1 = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForBLSampleWebServiceWsdl = Client(
self.strToolsForBLSampleWebServiceWsdl,
transport=httpAuthenticatedToolsForAutoprocessingWebService1,
cache=None)
httpAuthenticatedToolsForAutoprocessingWebService2 = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForScreeningEDNAWebServiceWsdl = Client(
self.strToolsForScreeningEDNAWebServiceWsdl,
transport=httpAuthenticatedToolsForAutoprocessingWebService2,
cache=None)
self.bContinue = True
# Data collection Id
if xsDataInputISPyBStoreScreening.screening.dataCollectionGroupId is None:
xsDataISPyBImage = xsDataInputISPyBStoreScreening.image
if xsDataISPyBImage is not None:
httpAuthenticatedToolsForAutoprocessingWebService3 = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=
httpAuthenticatedToolsForAutoprocessingWebService3,
cache=None)
self.iDataCollectionGroupId = self.findDataCollectionFromFileLocationAndFileName(
clientToolsForCollectionWebService,
xsDataISPyBImage.fileLocation.value,
xsDataISPyBImage.fileName.value)
if self.iDataCollectionGroupId is None:
self.ERROR("Couldn't obtain data collection id!")
self.setFailure()
else:
xsDataInputISPyBStoreScreening.screening.dataCollectionGroupId = XSDataInteger(
self.iDataCollectionGroupId)
else:
self.iDataCollectionGroupId = xsDataInputISPyBStoreScreening.screening.dataCollectionGroupId.value
if not self.isFailure():
# DiffractionPlan
xsDataISPyBDiffractionPlan = xsDataInputISPyBStoreScreening.diffractionPlan
iDiffractionPlanId = self.storeOrUpdateDiffractionPlan(
clientToolsForBLSampleWebServiceWsdl,
xsDataISPyBDiffractionPlan)
if iDiffractionPlanId is None:
self.ERROR(
"Couldn't create entry for diffraction plan in ISPyB!")
self.setFailure()
self.bContinue = False
# Screening
xsDataISPyBScreening = xsDataInputISPyBStoreScreening.screening
self.iScreeningId = self.storeOrUpdateScreening(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreening, iDiffractionPlanId)
if self.iScreeningId is None:
self.ERROR("Couldn't create entry for screening in ISPyB!")
self.setFailure()
self.bContinue = False
# Screening Output Container
for xsDataISPyBScreeningOutputContainer in xsDataInputISPyBStoreScreening.screeningOutputContainer:
xsDataISPyBScreeningOutput = xsDataISPyBScreeningOutputContainer.screeningOutput
iScreeningOutputId = self.storeOrUpdateScreeningOutput(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningOutput, self.iScreeningId)
if iScreeningOutputId is None:
self.ERROR("Couldn't create entry for screening in ISPyB!")
self.setFailure()
self.bContinue = False
for xsDataISPyBScreeningOutputLattice in xsDataISPyBScreeningOutputContainer.screeningOutputLattice:
iScreeningOutputLatticeId = self.storeOrUpdateScreeningOutputLattice(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningOutputLattice, iScreeningOutputId)
if iScreeningOutputLatticeId is None:
self.ERROR(
"Couldn't create entry for screening lattice in ISPyB!"
)
self.setFailure()
self.bContinue = False
for xsDataISPyBScreeningStrategyContainer in xsDataISPyBScreeningOutputContainer.screeningStrategyContainer:
# Create an empty object of type XSDataISPyBScreeningStrategy
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy(
)
iScreeningStrategyId = self.storeOrUpdateScreeningStrategy(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningStrategy, iScreeningOutputId)
if iScreeningStrategyId is None:
self.ERROR(
"Couldn't create entry for screening strategy in ISPyB!"
)
self.setFailure()
self.bContinue = False
for xsDataISPyBScreeningStrategyWedgeContainer in xsDataISPyBScreeningStrategyContainer.screeningStrategyWedgeContainer:
xsDataISPyBScreeningStrategyWedge = xsDataISPyBScreeningStrategyWedgeContainer.screeningStrategyWedge
iScreeningStrategyWedgeId = self.storeOrUpdateScreeningStrategyWedge(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningStrategyWedge,
iScreeningStrategyId)
if iScreeningStrategyWedgeId is None:
self.ERROR(
"Couldn't create entry for screening strategy in ISPyB!"
)
self.setFailure()
self.bContinue = False
for xsDataISPyBScreeningStrategySubWedge in xsDataISPyBScreeningStrategyWedgeContainer.screeningStrategySubWedge:
iScreeningStrategySubWedgeId = self.storeOrUpdateScreeningStrategySubWedge(
clientToolsForScreeningEDNAWebServiceWsdl,
xsDataISPyBScreeningStrategySubWedge,
iScreeningStrategyWedgeId)
if iScreeningStrategySubWedgeId is None:
self.ERROR(
"Couldn't create entry for screening strategy in ISPyB!"
)
self.setFailure()
self.bContinue = False