def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBGetSampleInformationv1_4.process")
# First get the image ID
xsDataInputGetSampleInformation = self.getDataInput()
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForBLSampleWebServiceWsdl = Client(self.strToolsForBLSampleWebServiceWsdl, transport=httpAuthenticatedToolsForCollectionWebService)
iSampleId = self.getXSValue(xsDataInputGetSampleInformation.sampleId)
sampleInfo = clientToolsForBLSampleWebServiceWsdl.service.getSampleInformation(iSampleId)
self.DEBUG("Sample info from ISPyB: %r" % sampleInfo)
if sampleInfo is not None:
if "code" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.code = XSDataString(sampleInfo.code)
if "cellA" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellA = XSDataDouble(sampleInfo.cellA)
if "cellB" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellB = XSDataDouble(sampleInfo.cellB)
if "cellC" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellC = XSDataDouble(sampleInfo.cellC)
if "cellAlpha" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellAlpha = XSDataDouble(sampleInfo.cellAlpha)
if "cellBeta" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellBeta = XSDataDouble(sampleInfo.cellBeta)
if "cellGamma" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.cellGamma = XSDataDouble(sampleInfo.cellGamma)
if "containerSampleChangerLocation" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.containerSampleChangerLocation = XSDataString(sampleInfo.containerSampleChangerLocation)
if "crystalSpaceGroup" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.crystalSpaceGroup = XSDataString(sampleInfo.crystalSpaceGroup)
if "experimentType" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.experimentType = XSDataString(sampleInfo.experimentType)
if "holderLength" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.holderLength = XSDataDouble(sampleInfo.holderLength)
if "minimalResolution" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.minimalResolution = XSDataDouble(sampleInfo.minimalResolution)
if "proteinAcronym" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.proteinAcronym = XSDataString(sampleInfo.proteinAcronym)
if "sampleId" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.sampleId = XSDataInteger(sampleInfo.sampleId)
if "sampleLocation" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.sampleLocation = XSDataString(sampleInfo.sampleLocation)
if "sampleName" in sampleInfo:
self.xsDataResultISPyBGetSampleInformation.sampleName = XSDataString(sampleInfo.sampleName)
if "diffractionPlan" in sampleInfo:
xsDataISPyBDiffractionPlan = XSDataISPyBDiffractionPlan()
if "aimedCompleteness" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.aimedCompleteness = XSDataDouble(sampleInfo.diffractionPlan.aimedCompleteness)
if "aimedIOverSigmaAtHighestResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.aimedIOverSigmaAtHighestResolution = XSDataDouble(sampleInfo.diffractionPlan.aimedIOverSigmaAtHighestResolution)
if "aimedMultiplicity" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.aimedMultiplicity = XSDataDouble(sampleInfo.diffractionPlan.aimedMultiplicity)
if "aimedResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.aimedResolution = XSDataDouble(sampleInfo.diffractionPlan.aimedResolution)
if "anomalousData" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.anomalousData = XSDataBoolean(sampleInfo.diffractionPlan.anomalousData)
if "comments" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.comments = XSDataString(sampleInfo.diffractionPlan.comments)
if "complexity" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.complexity = XSDataString(sampleInfo.diffractionPlan.complexity)
if "diffractionPlanId" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.diffractionPlanId = XSDataInteger(sampleInfo.diffractionPlan.diffractionPlanId)
if "estimateRadiationDamage" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.estimateRadiationDamage = XSDataBoolean(sampleInfo.diffractionPlan.estimateRadiationDamage)
if "experimentKind" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.experimentKind = XSDataString(sampleInfo.diffractionPlan.experimentKind)
if "exposureTime" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.exposureTime = XSDataDouble(sampleInfo.diffractionPlan.exposureTime)
if "forcedSpaceGroup" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.forcedSpaceGroup = XSDataString(sampleInfo.diffractionPlan.forcedSpaceGroup)
if "kappaStrategyOption" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.kappaStrategyOption = XSDataString(sampleInfo.diffractionPlan.kappaStrategyOption)
if "maxDimAccrossSpindleAxis" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.maxDimAccrossSpindleAxis = XSDataDouble(sampleInfo.diffractionPlan.maxDimAccrossSpindleAxis)
if "maximalResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.maximalResolution = XSDataDouble(sampleInfo.diffractionPlan.maximalResolution)
if "minDimAccrossSpindleAxis" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.minDimAccrossSpindleAxis = XSDataDouble(sampleInfo.diffractionPlan.minDimAccrossSpindleAxis)
if "minimalResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.minimalResolution = XSDataDouble(sampleInfo.diffractionPlan.minimalResolution)
if "numberOfPositions" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.numberOfPositions = XSDataInteger(sampleInfo.diffractionPlan.numberOfPositions)
if "observedResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.observedResolution = XSDataDouble(sampleInfo.diffractionPlan.observedResolution)
if "oscillationRange" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.oscillationRange = XSDataDouble(sampleInfo.diffractionPlan.oscillationRange)
if "preferredBeamSizeX" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.preferredBeamSizeX = XSDataDouble(sampleInfo.diffractionPlan.preferredBeamSizeX)
if "preferredBeamSizeY" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.preferredBeamSizeY = XSDataDouble(sampleInfo.diffractionPlan.preferredBeamSizeY)
if "radiationSensitivity" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.radiationSensitivity = XSDataDouble(sampleInfo.diffractionPlan.radiationSensitivity)
if "radiationSensitivityBeta" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.radiationSensitivityBeta = XSDataDouble(sampleInfo.diffractionPlan.radiationSensitivityBeta)
if "radiationSensitivityGamma" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.radiationSensitivityGamma = XSDataDouble(sampleInfo.diffractionPlan.radiationSensitivityGamma)
if "requiredCompleteness" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.requiredCompleteness = XSDataDouble(sampleInfo.diffractionPlan.requiredCompleteness)
if "requiredMultiplicity" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.requiredMultiplicity = XSDataDouble(sampleInfo.diffractionPlan.requiredMultiplicity)
if "requiredResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.requiredResolution = XSDataDouble(sampleInfo.diffractionPlan.requiredResolution)
if "screeningResolution" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.screeningResolution = XSDataDouble(sampleInfo.diffractionPlan.screeningResolution)
if "anomalousScatterer" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.anomalousScatterer = XSDataString(sampleInfo.diffractionPlan.anomalousScatterer)
if "strategyOption" in sampleInfo.diffractionPlan:
xsDataISPyBDiffractionPlan.strategyOption = XSDataString(sampleInfo.diffractionPlan.strategyOption)
self.xsDataResultISPyBGetSampleInformation.diffractionPlan = xsDataISPyBDiffractionPlan
self.DEBUG("EDPluginISPyBGetSampleInformationv1_4.process: result=%s" % pprint.pformat(self.xsDataResultISPyBGetSampleInformation))
def generateXSDataISPyBDiffractionPlan(_xsDataResultCharacterisation):
xsDataISPyBDiffractionPlan = None
xsDataCollection = _xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
if xsDataDiffractionPlan != None:
xsDataISPyBDiffractionPlan = XSDataISPyBDiffractionPlan()
xsDataISPyBDiffractionPlan.aimedCompleteness = xsDataDiffractionPlan.aimedCompleteness
xsDataISPyBDiffractionPlan.aimedIOverSigmaAtHighestResolution = xsDataDiffractionPlan.aimedIOverSigmaAtHighestResolution
xsDataISPyBDiffractionPlan.aimedMultiplicity = xsDataDiffractionPlan.aimedMultiplicity
xsDataISPyBDiffractionPlan.aimedResolution = xsDataDiffractionPlan.aimedResolution
xsDataISPyBDiffractionPlan.anomalousData = xsDataDiffractionPlan.anomalousData
xsDataISPyBDiffractionPlan.complexity = xsDataDiffractionPlan.complexity
xsDataISPyBDiffractionPlan.detectorDistanceMax = xsDataDiffractionPlan.detectorDistanceMax
xsDataISPyBDiffractionPlan.detectorDistanceMin = xsDataDiffractionPlan.detectorDistanceMin
xsDataISPyBDiffractionPlan.estimateRadiationDamage = xsDataDiffractionPlan.estimateRadiationDamage
xsDataISPyBDiffractionPlan.forcedSpaceGroup = xsDataDiffractionPlan.forcedSpaceGroup
xsDataISPyBDiffractionPlan.goniostatMaxOscillationSpeed = xsDataDiffractionPlan.goniostatMaxOscillationSpeed
xsDataISPyBDiffractionPlan.goniostatMinOscillationWidth = xsDataDiffractionPlan.goniostatMinOscillationWidth
strAllKappaStrategyOptions = ""
for kappaStrategyOption in xsDataDiffractionPlan.kappaStrategyOption:
strAllKappaStrategyOptions += kappaStrategyOption.value
# Add a comma to separate entries except for the last item
if kappaStrategyOption != xsDataDiffractionPlan.kappaStrategyOption[-1]:
strAllKappaStrategyOptions += ", "
if strAllKappaStrategyOptions != "":
xsDataISPyBDiffractionPlan.kappaStrategyOption = XSDataString(strAllKappaStrategyOptions)
xsDataISPyBDiffractionPlan.maxExposureTimePerDataCollection = xsDataDiffractionPlan.maxExposureTimePerDataCollection
xsDataISPyBDiffractionPlan.minExposureTimePerImage = xsDataDiffractionPlan.minExposureTimePerImage
xsDataISPyBDiffractionPlan.minTransmission = xsDataDiffractionPlan.minTransmission
xsDataISPyBDiffractionPlan.numberOfPositions = xsDataDiffractionPlan.numberOfPositions
xsDataISPyBDiffractionPlan.requiredCompleteness = xsDataDiffractionPlan.requiredCompleteness
xsDataISPyBDiffractionPlan.requiredMultiplicity = xsDataDiffractionPlan.requiredMultiplicity
xsDataISPyBDiffractionPlan.requiredResolution = xsDataDiffractionPlan.requiredResolution
xsDataISPyBDiffractionPlan.strategyOption = xsDataDiffractionPlan.strategyOption
return xsDataISPyBDiffractionPlan
def generateXSDataISPyBDiffractionPlan(_xsDataResultCharacterisation):
xsDataISPyBDiffractionPlan = None
xsDataCollection = _xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
xsDataDiffractionPlan = xsDataCollection.getDiffractionPlan()
if xsDataDiffractionPlan != None:
xsDataISPyBDiffractionPlan = XSDataISPyBDiffractionPlan()
xsDataISPyBDiffractionPlan.aimedCompleteness = xsDataDiffractionPlan.aimedCompleteness
xsDataISPyBDiffractionPlan.aimedIOverSigmaAtHighestResolution = xsDataDiffractionPlan.aimedIOverSigmaAtHighestResolution
xsDataISPyBDiffractionPlan.aimedMultiplicity = xsDataDiffractionPlan.aimedMultiplicity
xsDataISPyBDiffractionPlan.aimedResolution = xsDataDiffractionPlan.aimedResolution
xsDataISPyBDiffractionPlan.anomalousData = xsDataDiffractionPlan.anomalousData
xsDataISPyBDiffractionPlan.complexity = xsDataDiffractionPlan.complexity
xsDataISPyBDiffractionPlan.detectorDistanceMax = xsDataDiffractionPlan.detectorDistanceMax
xsDataISPyBDiffractionPlan.detectorDistanceMin = xsDataDiffractionPlan.detectorDistanceMin
xsDataISPyBDiffractionPlan.estimateRadiationDamage = xsDataDiffractionPlan.estimateRadiationDamage
xsDataISPyBDiffractionPlan.forcedSpaceGroup = xsDataDiffractionPlan.forcedSpaceGroup
xsDataISPyBDiffractionPlan.goniostatMaxOscillationSpeed = xsDataDiffractionPlan.goniostatMaxOscillationSpeed
xsDataISPyBDiffractionPlan.goniostatMinOscillationWidth = xsDataDiffractionPlan.goniostatMinOscillationWidth
strAllKappaStrategyOptions = ""
for kappaStrategyOption in xsDataDiffractionPlan.kappaStrategyOption:
strAllKappaStrategyOptions += kappaStrategyOption.value
# Add a comma to separate entries except for the last item
if kappaStrategyOption != xsDataDiffractionPlan.kappaStrategyOption[
-1]:
strAllKappaStrategyOptions += ", "
if strAllKappaStrategyOptions != "":
xsDataISPyBDiffractionPlan.kappaStrategyOption = XSDataString(
strAllKappaStrategyOptions)
xsDataISPyBDiffractionPlan.maxExposureTimePerDataCollection = xsDataDiffractionPlan.maxExposureTimePerDataCollection
xsDataISPyBDiffractionPlan.minExposureTimePerImage = xsDataDiffractionPlan.minExposureTimePerImage
xsDataISPyBDiffractionPlan.minTransmission = xsDataDiffractionPlan.minTransmission
xsDataISPyBDiffractionPlan.numberOfPositions = xsDataDiffractionPlan.numberOfPositions
xsDataISPyBDiffractionPlan.requiredCompleteness = xsDataDiffractionPlan.requiredCompleteness
xsDataISPyBDiffractionPlan.requiredMultiplicity = xsDataDiffractionPlan.requiredMultiplicity
xsDataISPyBDiffractionPlan.requiredResolution = xsDataDiffractionPlan.requiredResolution
xsDataISPyBDiffractionPlan.strategyOption = xsDataDiffractionPlan.strategyOption
return xsDataISPyBDiffractionPlan