def storeAutoProcProgram(self, _clientToolsForAutoprocessingWebService,
_xsDataAutoProcProgram):
"""Creates an entry in the ISPyB AutoProcProgram table"""
self.DEBUG("EDPluginISPyBStoreAutoProcv1_3.storeAutoProcProgram")
strProcessingCommandLine = self.getValue(
_xsDataAutoProcProgram.getProcessingCommandLine(), "")
strProcessingPrograms = self.getValue(
_xsDataAutoProcProgram.getProcessingPrograms(), "")
bProcessingStatus = self.getValue(
_xsDataAutoProcProgram.getProcessingStatus(), True)
strProcessingMessage = self.getValue(
_xsDataAutoProcProgram.getProcessingMessage(), "")
processingStartTime = self.getDateValue(
_xsDataAutoProcProgram.getProcessingStartTime(),
"%a %b %d %H:%M:%S %Y", DateTime(datetime.datetime.now()))
processingEndTime = self.getDateValue(
_xsDataAutoProcProgram.getProcessingEndTime(),
"%a %b %d %H:%M:%S %Y", DateTime(datetime.datetime.now()))
strProcessingEnvironment = self.getValue(
_xsDataAutoProcProgram.getProcessingEnvironment(), "")
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcProgramId = _clientToolsForAutoprocessingWebService.service.storeAutoProcProgram(
in0 = strProcessingCommandLine, \
in1 = strProcessingPrograms, \
in2 = bProcessingStatus, \
in3 = strProcessingMessage, \
in4 = processingStartTime, \
in5 = processingEndTime, \
in6 = strProcessingEnvironment, \
in7 = recordTimeStamp
)
self.DEBUG("AutoProcProgramId: %r" % iAutoProcProgramId)
return iAutoProcProgramId
def xml(self):
root = Element("Timestamp", ns=wsuns)
created = Element('Created', ns=wsuns)
created.setText(str(DateTime(self.created)))
expires = Element('Expires', ns=wsuns)
expires.setText(str(DateTime(self.expires)))
root.append(created)
root.append(expires)
return root
def translate(self, value, topython=True):
if topython:
if isinstance(value, six.string_types) and len(value):
return DateTime(value).datetime
else:
return None
else:
if isinstance(value, dt.date):
return str(DateTime(value))
else:
return value
def getDateValue(self, _strValue, _strFormat, _oDefaultValue):
if _strValue is None:
oReturnValue = _oDefaultValue
else:
try:
oReturnValue = DateTime(
datetime.datetime.strptime(_strValue, _strFormat))
except:
oReturnValue = DateTime(
datetime.datetime.strptime(_strValue, _strFormat))
return oReturnValue
def xml(self):
"""
Get xml representation of the object.
@return: The root node.
@rtype: L{Element}
"""
root = Element('UsernameToken', ns=wssens)
u = Element('Username', ns=wssens)
u.setText(self.username)
root.append(u)
p = Element('Password', ns=wssens)
p.setText(self.password)
if self.password_digest:
p.set("Type", wsdigest)
p.setText(self.password_digest)
else:
p.set("Type", wstext)
root.append(p)
if self.nonce is not None:
n = Element('Nonce', ns=wssens)
if self.nonce_has_encoding:
n.set("EncodingType", nonce_encoding_type)
n.setText(self.nonce)
root.append(n)
if self.created is not None:
n = Element('Created', ns=wsuns)
n.setText(str(DateTime(self.created)))
root.append(n)
return root
def storeOrUpdateAutoProc(self, _clientToolsForAutoprocessingWebService,
_xsDataAutoProc):
"""Creates an entry in the ISPyB AutoProc table"""
iAutoProcId = self.getXSValue(_xsDataAutoProc.getAutoProcId())
iAutoProcProgramId = self.iAutoProcProgramId
strSpaceGroup = self.getXSValue(_xsDataAutoProc.getSpaceGroup())
fRefinedCellA = self.getXSValue(_xsDataAutoProc.getRefinedCell_a())
fRefinedCellB = self.getXSValue(_xsDataAutoProc.getRefinedCell_b())
fRefinedCellC = self.getXSValue(_xsDataAutoProc.getRefinedCell_c())
fRefinedCellAlpha = self.getXSValue(
_xsDataAutoProc.getRefinedCell_alpha())
fRefinedCellBeta = self.getXSValue(
_xsDataAutoProc.getRefinedCell_beta())
fRefinedCellGamma = self.getXSValue(
_xsDataAutoProc.getRefinedCell_gamma())
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcId = _clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProc(
arg0=iAutoProcId, \
autoProcProgramId=iAutoProcProgramId, \
spaceGroup=strSpaceGroup, \
refinedCellA=fRefinedCellA, \
refinedCellB=fRefinedCellB, \
refinedCellC=fRefinedCellC, \
refinedCellAlpha=fRefinedCellAlpha, \
refinedCellBeta=fRefinedCellBeta, \
refinedCellGamma=fRefinedCellGamma, \
recordTimeStamp=recordTimeStamp \
)
self.DEBUG("AutoProcId: %r" % iAutoProcId)
return iAutoProcId
def process(self, _edObject=None):
"""
Uses ToolsForCollectionWebService for storing the workflow status
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreWorkflowv1_4.process")
# First get the image ID
xsDataWorkflow = self.getDataInput().getWorkflow()
httpAuthenticatedToolsForCollectionWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForCollectionWebService = Client(
self.strToolsForCollectionWebServiceWsdl,
transport=httpAuthenticatedToolsForCollectionWebService)
workflow3VO = clientToolsForCollectionWebService.factory.create(
'workflow3VO')
workflow3VO.comments = self.getXSValue(xsDataWorkflow.comments)
workflow3VO.logFilePath = self.getXSValue(xsDataWorkflow.logFilePath)
workflow3VO.recordTimeStamp = self.getDateValue(
xsDataWorkflow.recordTimeStamp, "%a %b %d %H:%M:%S %Y",
DateTime(datetime.datetime.now()))
workflow3VO.resultFilePath = self.getXSValue(
xsDataWorkflow.resultFilePath)
workflow3VO.status = self.getXSValue(xsDataWorkflow.status)
workflow3VO.workflowId = self.getXSValue(xsDataWorkflow.workflowId)
workflow3VO.workflowTitle = self.getXSValue(
xsDataWorkflow.workflowTitle)
workflow3VO.workflowType = self.getXSValue(xsDataWorkflow.workflowType)
# print workflow3VO
self.iWorkflowId = clientToolsForCollectionWebService.service.storeOrUpdateWorkflow(
workflow3VO)
self.DEBUG("EDPluginISPyBStoreWorkflowv1_4.process: WorkflowId=%d" %
self.iWorkflowId)
def process(self, _edObject=None):
"""
First uses the ImageService to find the imageId.
Then uses ToolsForCollectionWebService for storing the image quality indicators.
"""
EDPluginExec.process(self)
self.DEBUG("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.process")
httpAuthenticatedToolsForAutoprocessingWebService = HttpAuthenticated(username=self.strUserName, password=self.strPassWord)
clientToolsForAutoprocessingWebService = Client(self.strToolsForAutoprocessingWebServiceWsdl, transport=httpAuthenticatedToolsForAutoprocessingWebService)
# Loop over all input image quality indicators:
listImageQualityIndicatorsForWS = []
for xsDataImageQualityIndicators in self.dataInput.imageQualityIndicators:
#print xsDataImageQualityIndicators.marshal()
imageQualityIndicatorsWS3VO = clientToolsForAutoprocessingWebService.factory.create('imageQualityIndicatorsWS3VO')
strPathToImage = xsDataImageQualityIndicators.getImage().getPath().getValue()
imageQualityIndicatorsWS3VO.fileName = os.path.basename(strPathToImage)
imageQualityIndicatorsWS3VO.fileLocation = os.path.dirname(strPathToImage)
# imageQualityIndicatorsWS3VO.imageId = 0
imageQualityIndicatorsWS3VO.autoProcProgramId = self.iAutoProcProgramId
imageQualityIndicatorsWS3VO.spotTotal = self.getXSValue(xsDataImageQualityIndicators.spotTotal)
imageQualityIndicatorsWS3VO.inResTotal = self.getXSValue(xsDataImageQualityIndicators.inResTotal)
imageQualityIndicatorsWS3VO.goodBraggCandidates = self.getXSValue(xsDataImageQualityIndicators.goodBraggCandidates)
imageQualityIndicatorsWS3VO.iceRings = self.getXSValue(xsDataImageQualityIndicators.iceRings)
imageQualityIndicatorsWS3VO.method1Res = self.getXSValue(xsDataImageQualityIndicators.method1Res)
imageQualityIndicatorsWS3VO.method2Res = self.getXSValue(xsDataImageQualityIndicators.method2Res)
imageQualityIndicatorsWS3VO.maxUnitCell = self.getXSValue(xsDataImageQualityIndicators.maxUnitCell)
imageQualityIndicatorsWS3VO.pctSaturationTop50Peaks = self.getXSValue(xsDataImageQualityIndicators.pctSaturationTop50Peaks)
imageQualityIndicatorsWS3VO.inResolutionOvrlSpots = self.getXSValue(xsDataImageQualityIndicators.inResolutionOvrlSpots)
imageQualityIndicatorsWS3VO.binPopCutOffMethod2Res = self.getXSValue(xsDataImageQualityIndicators.binPopCutOffMethod2Res)
imageQualityIndicatorsWS3VO.totalIntegratedSignal = self.getXSValue(xsDataImageQualityIndicators.totalIntegratedSignal)
imageQualityIndicatorsWS3VO.recordTimeStamp = DateTime(datetime.datetime.now())
listImageQualityIndicatorsForWS.append(imageQualityIndicatorsWS3VO)
self.listImageQualityIndicatorsId = clientToolsForAutoprocessingWebService.service.storeOrUpdateImageQualityIndicatorsForFileNames(
listImageQualityIndicatorsForWS = listImageQualityIndicatorsForWS)
self.DEBUG("EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4.process: listImageQualityIndicatorsId=%r" % self.listImageQualityIndicatorsId)
def storeAutoProc(self, _clientToolsForAutoprocessingWebService,
_xsDataAutoProc):
"""Creates an entry in the ISPyB AutoProc table"""
iAutoProcProgramId = self.iAutoProcProgramId
strSpaceGroup = self.getValue(_xsDataAutoProc.getSpaceGroup(), "")
fRefinedCellA = self.getValue(_xsDataAutoProc.getRefinedCell_a(), -1)
fRefinedCellB = self.getValue(_xsDataAutoProc.getRefinedCell_b(), -1)
fRefinedCellC = self.getValue(_xsDataAutoProc.getRefinedCell_c(), -1)
fRefinedCellAlpha = self.getValue(
_xsDataAutoProc.getRefinedCell_alpha(), -1)
fRefinedCellBeta = self.getValue(_xsDataAutoProc.getRefinedCell_beta(),
-1)
fRefinedCellGamma = self.getValue(
_xsDataAutoProc.getRefinedCell_gamma(), -1)
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcId = _clientToolsForAutoprocessingWebService.service.storeAutoProc(
in0 = iAutoProcProgramId, \
in1 = strSpaceGroup, \
in2 = fRefinedCellA, \
in3 = fRefinedCellB, \
in4 = fRefinedCellC, \
in5 = fRefinedCellAlpha, \
in6 = fRefinedCellBeta, \
in7 = fRefinedCellGamma, \
in8 = recordTimeStamp \
)
self.DEBUG("AutoProcId: %r" % iAutoProcId)
return iAutoProcId
def storeOrUpdateScreening(self,
_clientToolsForScreeningEDNAWebServiceWsdl,
_xsDataISPyBScreening, _iDiffractionPlanId):
"""Creates an entry in ISPyB for the Screening table"""
self.DEBUG("EDPluginISPyBStoreScreeningv1_4.storeScreening")
iScreeningId = self.getXSValue(_xsDataISPyBScreening.screeningId)
iDataCollectionId = self.getXSValue(
_xsDataISPyBScreening.dataCollectionId)
iDiffractionPlanId = _iDiffractionPlanId
strTimeStamp = DateTime(datetime.datetime.now())
strProgramVersion = self.getXSValue(
_xsDataISPyBScreening.programVersion, _iMaxStringLength=45)
strComments = self.getXSValue(_xsDataISPyBScreening.comments,
_iMaxStringLength=255)
strShortComments = self.getXSValue(_xsDataISPyBScreening.shortComments,
_iMaxStringLength=20)
strXmlSampleInformation = self.getXSValue(
_xsDataISPyBScreening.xmlSampleInformation)
iScreeningId = _clientToolsForScreeningEDNAWebServiceWsdl.service.storeOrUpdateScreening(
iScreeningId, \
iDataCollectionId, \
iDiffractionPlanId, \
strTimeStamp, \
strProgramVersion, \
strComments, \
strShortComments, \
strXmlSampleInformation, \
)
self.DEBUG("ScreeningId: %d" % iScreeningId)
return iScreeningId
def storeOrUpdateAutoProcProgramAttachment(
self, _clientToolsForAutoprocessingWebService,
_xsDataAutoProcProgramAttachment):
"""Creates an entry in the ISPyB AutoProcProgramAttachment table"""
iAutoProcProgramAttachmentId = self.getXSValue(
_xsDataAutoProcProgramAttachment.getAutoProcProgramAttachmentId())
strFileType = self.getXSValue(
_xsDataAutoProcProgramAttachment.getFileType())
strFileName = self.getXSValue(
_xsDataAutoProcProgramAttachment.getFileName())
strFilePath = self.getXSValue(
_xsDataAutoProcProgramAttachment.getFilePath())
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcProgramId = self.iAutoProcProgramId
iAutoProcProgramAttachmentId = _clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProcProgramAttachment(
arg0=iAutoProcProgramAttachmentId, \
fileType=strFileType, \
fileName=strFileName, \
filePath=strFilePath, \
recordTimeStamp=recordTimeStamp, \
autoProcProgramId=iAutoProcProgramId
)
self.DEBUG("AutoProcProgramAttachmentId: %r" %
iAutoProcProgramAttachmentId)
return iAutoProcProgramAttachmentId
def storeOrUpdateAutoProcProgram(self,
_clientToolsForAutoprocessingWebService,
_xsDataAutoProcProgram):
"""Creates an entry in the ISPyB AutoProcProgram table"""
self.DEBUG(
"EDPluginISPyBStoreAutoProcv1_4.storeOrUpdateAutoProcProgram")
iAutoProcProgramId = self.getXSValue(
_xsDataAutoProcProgram.getAutoProcProgramId())
strProcessingCommandLine = self.getXSValue(
_xsDataAutoProcProgram.getProcessingCommandLine())
strProcessingPrograms = self.getXSValue(
_xsDataAutoProcProgram.getProcessingPrograms())
strProcessingStatus = self.getXSValue(
_xsDataAutoProcProgram.getProcessingStatus(), "SUCCESS")
if strProcessingStatus == "true" or strProcessingStatus == "1":
strProcessingStatus = "SUCCESS"
elif strProcessingStatus == "false" or strProcessingStatus == "0":
strProcessingStatus = "FAILED"
strProcessingMessage = self.getXSValue(
_xsDataAutoProcProgram.getProcessingMessage())
processingStartTime = self.getDateValue(
_xsDataAutoProcProgram.getProcessingStartTime(),
"%a %b %d %H:%M:%S %Y", DateTime(datetime.datetime.now()))
processingEndTime = self.getDateValue(
_xsDataAutoProcProgram.getProcessingEndTime(),
"%a %b %d %H:%M:%S %Y", DateTime(datetime.datetime.now()))
strProcessingEnvironment = self.getXSValue(
_xsDataAutoProcProgram.getProcessingEnvironment())
recordTimeStamp = self.getDateValue(None, "%a %b %d %H:%M:%S %Y",
DateTime(datetime.datetime.now()))
iAutoProcProgramId = _clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProcProgram(
arg0=iAutoProcProgramId,
processingCommandLine=strProcessingCommandLine,
processingPrograms=strProcessingPrograms,
processingStatus=strProcessingStatus,
processingMessage=strProcessingMessage,
processingStartTime=processingStartTime,
processingEndTime=processingEndTime,
processingEnvironment=strProcessingEnvironment,
recordTimeStamp=recordTimeStamp)
self.DEBUG("AutoProcProgramId: %r" % iAutoProcProgramId)
return iAutoProcProgramId
def storeOrUpdateAutoProcIntegration(self, _clientToolsForAutoprocessingWebService, \
_iAutoProcIntegrationId=None, _iDataCollectionId=None):
"""Creates or updates an entry in the ISPyB AutoProcIntegration table"""
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcIntegrationId = _clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProcIntegration(
arg0 = _iAutoProcIntegrationId, \
recordTimeStamp= recordTimeStamp, \
dataCollectionId = _iDataCollectionId \
)
self.DEBUG("AutoProcProgramIntegrationId: %r" % iAutoProcIntegrationId)
return iAutoProcIntegrationId
def storeOrUpdateAutoProcScalingHasIntId(
self, _clientToolsForAutoprocessingWebService):
"""Creates an entry in the ISPyB storeOrUpdateAutoProcScalingHasIntId table"""
iAutoProcIntegrationId = self.iAutoProcIntegrationId
iAutoProcScalingId = self.iAutoProcScalingId
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcScalingHasIntId = _clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProcScalingHasInt(
arg0=None,
autoProcIntegrationId=iAutoProcIntegrationId,
autoProcScalingId=iAutoProcScalingId,
recordTimeStamp=recordTimeStamp)
self.DEBUG("AutoProcScalingHasIntId: %r" % iAutoProcScalingHasIntId)
return iAutoProcScalingHasIntId
def storeAutoProcScaling(self, _clientToolsForAutoprocessingWebService,
_xsDataAutoProcScaling):
"""Creates an entry in the ISPyB AutoProcScaling table"""
iAutoProcId = self.iAutoProcId
recordTimeStamp = self.getDateValue(
_xsDataAutoProcScaling.getRecordTimeStamp(), "%Y-%m-%d %H:%M:%S",
DateTime(datetime.datetime.now()))
iAutoProcScalingId = _clientToolsForAutoprocessingWebService.service.storeAutoProcScaling(
in0 = iAutoProcId, \
in1 = recordTimeStamp \
)
self.DEBUG("AutoProcScalingId: %r" % iAutoProcScalingId)
return iAutoProcScalingId
def storeAutoProcScaling_has_IntId(
self, _clientToolsForAutoprocessingWebService):
"""Creates an entry in the ISPyB storeAutoProcScaling_has_IntId table"""
iAutoProcIntegrationId = self.iAutoProcIntegrationId
iAutoProcScalingId = self.iAutoProcScalingId
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcScaling_has_intId = _clientToolsForAutoprocessingWebService.service.storeAutoProcScalingHasInt(
in0 = iAutoProcIntegrationId, \
in1 = iAutoProcScalingId, \
in2 = recordTimeStamp \
)
self.DEBUG("AutoProcScaling_has_IntId: %r" %
iAutoProcScaling_has_intId)
return iAutoProcScaling_has_intId
def storeOrUpdateAutoProcStatus(self, _clientToolsForAutoprocessingWebService, \
_xsDataAutoProcStatus, _iAutoProcIntegrationId, _iAutoProcStatusId=None):
"""Creates or updates an entry in the ISPyB AutoProcIntegration table"""
strStep = self.getXSValue(_xsDataAutoProcStatus.getStep())
strStatus = self.getXSValue(_xsDataAutoProcStatus.getStatus())
strComments = self.getXSValue(_xsDataAutoProcStatus.getComments(),
_iMaxStringLength=1024)
strBltimeStamp = DateTime(datetime.datetime.now())
iAutoProcIntegrationId = _clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProcStatus(
arg0=_iAutoProcStatusId, \
autoProcIntegrationId=_iAutoProcIntegrationId, \
step=strStep, \
status=strStatus, \
comments=strComments, \
bltimeStamp=strBltimeStamp, \
)
self.DEBUG("AutoProcProgramStatusId: %r" % iAutoProcIntegrationId)
return iAutoProcIntegrationId
def xml(self):
"""
Get xml representation of the object.
@return: The root node.
@rtype: L{Element}
"""
root = Element('UsernameToken', ns=wssens)
u = Element('Username', ns=wssens)
u.setText(self.username)
root.append(u)
p = Element('Password', ns=wssens)
p.setText(self.password)
root.append(p)
if self.nonce is not None:
n = Element('Nonce', ns=wssens)
n.setText(self.nonce)
root.append(n)
if self.created is not None:
n = Element('Created', ns=wsuns)
n.setText(str(DateTime(self.created)))
root.append(n)
return root
def storeAutoProcProgramAttachment(self,
_clientToolsForAutoprocessingWebService,
_xsDataAutoProcProgramAttachment):
"""Creates an entry in the ISPyB AutoProcProgramAttachment table"""
iAutoProcProgramId = self.iAutoProcProgramId
strFileType = self.getValue(
_xsDataAutoProcProgramAttachment.getFileType(), "")
strFileName = self.getValue(
_xsDataAutoProcProgramAttachment.getFileName(), "")
strFilePath = self.getValue(
_xsDataAutoProcProgramAttachment.getFilePath(), "")
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcProgramAttachmentId = _clientToolsForAutoprocessingWebService.service.storeAutoProcProgramAttachment(
in0 = strFileType, \
in1 = strFileName, \
in2 = strFilePath, \
in3 = recordTimeStamp, \
in4 = iAutoProcProgramId
)
self.DEBUG("AutoProcProgramAttachmentId: %r" %
iAutoProcProgramAttachmentId)
return iAutoProcProgramAttachmentId
def storeOrUpdateScreeningOutputLattice(
self, _clientToolsForScreeningEDNAWebServiceWsdl,
_xsDataISPyBScreeningOutputLattice, _iScreeningOutputId):
"""Creates an entry in ISPyB for the ScreeningOutputLattice table"""
self.DEBUG(
"EDPluginISPyBStoreScreeningv1_4.storeScreeningOutputLattice")
iScreeningOutputLatticeId = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.screeningOutputLatticeId)
iScreeningOutputId = _iScreeningOutputId
strSpaceGroup = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.spaceGroup,
_iMaxStringLength=45)
strPointGroup = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.pointGroup,
_iMaxStringLength=45)
strBravaisLattice = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.bravaisLattice,
_iMaxStringLength=45)
fRawOrientationMatrix_a_x = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_a_x)
fRawOrientationMatrix_a_y = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_a_y)
fRawOrientationMatrix_a_z = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_a_z)
fRawOrientationMatrix_b_x = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_b_x)
fRawOrientationMatrix_b_y = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_b_y)
fRawOrientationMatrix_b_z = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_b_z)
fRawOrientationMatrix_c_x = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_c_x)
fRawOrientationMatrix_c_y = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_c_y)
fRawOrientationMatrix_c_z = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.rawOrientationMatrix_c_z)
fUnitCell_a = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.unitCell_a)
fUnitCell_b = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.unitCell_b)
fUnitCell_c = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.unitCell_c)
fUnitCell_alpha = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.unitCell_alpha)
fUnitCell_beta = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.unitCell_beta)
fUnitCell_gamma = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.unitCell_gamma)
strTimeStamp = DateTime(datetime.datetime.now())
bLabelitIndexing = self.getXSValue(
_xsDataISPyBScreeningOutputLattice.labelitIndexing,
_oDefaultValue=False)
iScreeningOutputLatticeId = _clientToolsForScreeningEDNAWebServiceWsdl.service.storeOrUpdateScreeningOutputLattice(
iScreeningOutputLatticeId, \
iScreeningOutputId, \
strSpaceGroup, \
strPointGroup, \
strBravaisLattice, \
fRawOrientationMatrix_a_x, \
fRawOrientationMatrix_a_y, \
fRawOrientationMatrix_a_z, \
fRawOrientationMatrix_b_x, \
fRawOrientationMatrix_b_y, \
fRawOrientationMatrix_b_z, \
fRawOrientationMatrix_c_x, \
fRawOrientationMatrix_c_y, \
fRawOrientationMatrix_c_z, \
fUnitCell_a, \
fUnitCell_b, \
fUnitCell_c, \
fUnitCell_alpha, \
fUnitCell_beta, \
fUnitCell_gamma, \
strTimeStamp, \
bLabelitIndexing, \
)
self.DEBUG("ScreeningOutputLatticeId: %d" % iScreeningOutputLatticeId)
return iScreeningOutputLatticeId
def testConstructFromString_timezone(self, string, y, M, d, h, m, s,
micros, tz_h, tz_m):
tzdelta = datetime.timedelta(hours=tz_h, minutes=tz_m)
tzinfo = FixedOffsetTimezone(tzdelta)
ref = datetime.datetime(y, M, d, h, m, s, micros, tzinfo=tzinfo)
assert DateTime(string).value == ref
def testConvertToString(self, input, output):
assert str(DateTime(input)) == output
def testConstructFromString(self, string, y, M, d, h, m, s, micros):
assert DateTime(string).value == datetime.datetime(
y, M, d, h, m, s, micros)
def testConstructFromString_subsecondRounding(self, string, y, M, d, h, m,
s, micros):
ref = datetime.datetime(y, M, d, h, m, s, micros)
assert DateTime(string).value == ref
def process(self, _edObject=None):
"""
Stores the contents of the AutoProcContainer in ISPyB.
"""
EDPluginISPyBv1_4.process(self)
iDataCollectionId = None
self.DEBUG("EDPluginISPyBStoreAutoProcStatusv1_4.process")
httpAuthenticatedToolsForAutoprocessingWebService = HttpAuthenticated(
username=self.strUserName, password=self.strPassWord)
clientToolsForAutoprocessingWebService = Client(
self.strToolsForAutoprocessingWebServiceWsdl,
transport=httpAuthenticatedToolsForAutoprocessingWebService,
cache=None)
xsDataInputStoreAutoProcStatus = self.getDataInput()
if xsDataInputStoreAutoProcStatus.dataCollectionId is not None:
iDataCollectionId = xsDataInputStoreAutoProcStatus.dataCollectionId
if xsDataInputStoreAutoProcStatus.autoProcIntegrationId is not None:
self.iAutoProcIntegrationId = xsDataInputStoreAutoProcStatus.autoProcIntegrationId
if xsDataInputStoreAutoProcStatus.autoProcStatusId is not None:
self.iAutoProcStatusId = xsDataInputStoreAutoProcStatus.autoProcStatusId
if xsDataInputStoreAutoProcStatus.anomalous is not None:
self.bAnomalous = xsDataInputStoreAutoProcStatus.anomalous
# If autoProcIntegrationId is not given a dataCollectionId must be present:
if (self.iAutoProcIntegrationId is None) and (iDataCollectionId is
None):
strErrorMessage = "Either data collection id or auto proc integration id must be given as input!"
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
else:
if self.iAutoProcIntegrationId is None:
# Check if we have AutoProcProgram
xsDataAutoProcProgram = xsDataInputStoreAutoProcStatus.AutoProcProgram
if xsDataAutoProcProgram is not None:
iAutoProcProgramId = self.getXSValue(
xsDataAutoProcProgram.getAutoProcProgramId())
strProcessingCommandLine = self.getXSValue(
xsDataAutoProcProgram.getProcessingCommandLine())
strProcessingPrograms = self.getXSValue(
xsDataAutoProcProgram.getProcessingPrograms())
strProcessingStatus = self.getXSValue(
xsDataAutoProcProgram.getProcessingStatus(), "SUCCESS")
if strProcessingStatus == "true" or strProcessingStatus == "1":
strProcessingStatus = "SUCCESS"
elif strProcessingStatus == "false" or strProcessingStatus == "0":
strProcessingStatus = "FAILED"
strProcessingMessage = self.getXSValue(
xsDataAutoProcProgram.getProcessingMessage())
processingStartTime = self.getDateValue(
xsDataAutoProcProgram.getProcessingStartTime(),
"%a %b %d %H:%M:%S %Y",
DateTime(datetime.datetime.now()))
processingEndTime = self.getDateValue(
xsDataAutoProcProgram.getProcessingEndTime(),
"%a %b %d %H:%M:%S %Y",
DateTime(datetime.datetime.now()))
strProcessingEnvironment = self.getXSValue(
xsDataAutoProcProgram.getProcessingEnvironment())
recordTimeStamp = self.getDateValue(
None, "%a %b %d %H:%M:%S %Y",
DateTime(datetime.datetime.now()))
self.iAutoProcProgramId = clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProcProgram(
arg0=iAutoProcProgramId, \
processingCommandLine=strProcessingCommandLine, \
processingPrograms=strProcessingPrograms, \
processingStatus=strProcessingStatus, \
processingMessage=strProcessingMessage, \
processingStartTime=processingStartTime, \
processingEndTime=processingEndTime, \
processingEnvironment=strProcessingEnvironment, \
recordTimeStamp=recordTimeStamp
)
else:
self.iAutoProcProgramId = None
self.DEBUG("iAutoProcProgramId: {0}".format(
self.iAutoProcProgramId))
# If no autoProcessingId is given create a dummy entry in the integration table
self.iAutoProcIntegrationId = self.storeOrUpdateAutoProcIntegration(clientToolsForAutoprocessingWebService,
_iDataCollectionId=iDataCollectionId,
_iAutoProcProgramId=self.iAutoProcProgramId, \
_bAnomalous=self.bAnomalous)
# Store the AutoProcStatus
self.iAutoProcStatusId = self.storeOrUpdateAutoProcStatus(clientToolsForAutoprocessingWebService, \
_xsDataAutoProcStatus=xsDataInputStoreAutoProcStatus.getAutoProcStatus(), \
_iAutoProcIntegrationId=self.iAutoProcIntegrationId, \
_iAutoProcStatusId=self.iAutoProcStatusId)
def testConstructFromDateTime(self):
dt = datetime.datetime(2001, 12, 10, 1, 1)
assert DateTime(dt).value is dt
dt.replace(tzinfo=UtcTimezone())
assert DateTime(dt).value is dt
def setcreated(self, *args, **kwargs):
UsernameToken.setcreated(self, *args, **kwargs)
if self.created is None:
self.created = dt.datetime.utcnow()
self.created = str(DateTime(self.created))
def storeDataCollectionProgram(self, _clientToolsForCollectionWebService,
_xsDataInputStoreDataCollection):
"""Creates an entry in the ISPyB DataCollectionProgram table"""
self.DEBUG(
"EDPluginISPyBStoreDataCollectionv1_4.storeDataCollectionProgram")
dataCollection = _xsDataInputStoreDataCollection.getDataCollection()
dataCollectionWS3VO = _clientToolsForCollectionWebService.factory.create(
'dataCollectionWS3VO')
dataCollectionWS3VO.dataCollectionId = self.getValue(
dataCollection.getDataCollectionId(), 0) # integer
dataCollectionWS3VO.blSampleId = self.getValue(
dataCollection.getBlSampleId(), 0) # integer
dataCollectionWS3VO.sessionId = self.getValue(
dataCollection.getSessionId()) # integer
dataCollectionWS3VO.experimentType = self.getValue(
dataCollection.getExperimentType()) # string
dataCollectionWS3VO.dataCollectionNumber = self.getValue(
dataCollection.getDataCollectionNumber()) # integer
dataCollectionWS3VO.startTime = DateTime(
self.getValue(dataCollection.getStartDate())) # string
dataCollectionWS3VO.endTime = DateTime(
self.getValue(dataCollection.getEndDate())) # string
dataCollectionWS3VO.runStatus = self.getValue(
dataCollection.getRunStatus()) # string
dataCollectionWS3VO.rotationAxis = self.getValue(
dataCollection.getRotationAxis()) # string
dataCollectionWS3VO.phiStart = self.getValue(
dataCollection.getPhiStart()) # float
dataCollectionWS3VO.kappaStart = self.getValue(
dataCollection.getKappaStart()) # float
dataCollectionWS3VO.omegaStart = self.getValue(
dataCollection.getOmegaStart()) # float
dataCollectionWS3VO.axisStart = self.getValue(
dataCollection.getAxisStart()) # float
dataCollectionWS3VO.axisEnd = self.getValue(
dataCollection.getAxisEnd()) # float
dataCollectionWS3VO.axisRange = self.getValue(
dataCollection.getAxisRange()) # float
dataCollectionWS3VO.overlap = self.getValue(
dataCollection.getOverlap()) # float
dataCollectionWS3VO.numberOfImages = self.getValue(
dataCollection.getNumberOfImages()) # integer
dataCollectionWS3VO.startImageNumber = self.getValue(
dataCollection.getStartImageNumber()) # integer
dataCollectionWS3VO.numberOfPasses = self.getValue(
dataCollection.getNumberOfPasses()) # integer
dataCollectionWS3VO.exposureTime = self.getValue(
dataCollection.getExposureTime()) # float
dataCollectionWS3VO.imageDirectory = self.getValue(
dataCollection.getImageDirectory()) # string
dataCollectionWS3VO.imagePrefix = self.getValue(
dataCollection.getImagePrefix()) # string
dataCollectionWS3VO.imageSuffix = self.getValue(
dataCollection.getImageSuffix()) # string
dataCollectionWS3VO.fileTemplate = self.getValue(
dataCollection.getFileTemplate()) # string
dataCollectionWS3VO.wavelength = self.getValue(
dataCollection.getWavelength()) # float
dataCollectionWS3VO.resolution = self.getValue(
dataCollection.getResolution()) # float
dataCollectionWS3VO.resolutionAtCorner = self.getValue(
dataCollection.getResolutionAtCorner()) # float
dataCollectionWS3VO.detectorDistance = self.getValue(
dataCollection.getDetectorDistance()) # float
dataCollectionWS3VO.detector2theta = self.getValue(
dataCollection.getDetector2theta()) # float
dataCollectionWS3VO.detectorMode = self.getValue(
dataCollection.getDetectorMode()) # string
dataCollectionWS3VO.undulatorGap1 = self.getValue(
dataCollection.getUndulatorGap1()) # float
dataCollectionWS3VO.undulatorGap2 = self.getValue(
dataCollection.getUndulatorGap2()) # float
dataCollectionWS3VO.undulatorGap3 = self.getValue(
dataCollection.getUndulatorGap3()) # float
dataCollectionWS3VO.xbeam = self.getValue(
dataCollection.getXbeam()) # float
dataCollectionWS3VO.ybeam = self.getValue(
dataCollection.getYbeam()) # float
dataCollectionWS3VO.crystalClass = self.getValue(
dataCollection.getCrystalClass()) # string
dataCollectionWS3VO.slitGapVertical = self.getValue(
dataCollection.getSlitGapVertical()) # float
dataCollectionWS3VO.slitGapHorizontal = self.getValue(
dataCollection.getSlitGapHorizontal()) # float
dataCollectionWS3VO.beamSizeAtSampleX = self.getValue(
dataCollection.getBeamSizeAtSampleX()) # float
dataCollectionWS3VO.beamSizeAtSampleY = self.getValue(
dataCollection.getBeamSizeAtSampleY()) # float
dataCollectionWS3VO.transmission = self.getValue(
dataCollection.getTransmission()) # float
dataCollectionWS3VO.synchrotronMode = self.getValue(
dataCollection.getSynchrotronMode()) # string
dataCollectionWS3VO.centeringMethod = self.getValue(
dataCollection.getCenteringMethod()) # string
dataCollectionWS3VO.averageTemperature = self.getValue(
dataCollection.getAverageTemperature()) # float
dataCollectionWS3VO.comments = self.getValue(
dataCollection.getComments()) # string
#printableForReport = str(self.getValue(dataCollection.getPrintableForReport())).lower() # boolean
if self.getValue(dataCollection.getPrintableForReport()):
dataCollectionWS3VO.printableForReport = 1
else:
dataCollectionWS3VO.printableForReport = 0
dataCollectionWS3VO.xtalSnapshotFullPath1 = self.getValue(
dataCollection.getXtalSnapshotFullPath1()) # string
dataCollectionWS3VO.xtalSnapshotFullPath2 = self.getValue(
dataCollection.getXtalSnapshotFullPath2()) # string
dataCollectionWS3VO.xtalSnapshotFullPath3 = self.getValue(
dataCollection.getXtalSnapshotFullPath3()) # string
dataCollectionWS3VO.xtalSnapshotFullPath4 = self.getValue(
dataCollection.getXtalSnapshotFullPath4()) # string
dataCollectionWS3VO.beamShape = self.getValue(
dataCollection.getBeamShape()) # string
iDataCollectionId = _clientToolsForCollectionWebService.service.storeOrUpdateDataCollection(
dataCollection=dataCollectionWS3VO)
self.DEBUG("DataCollectionProgramId: %r" % iDataCollectionId)
return iDataCollectionId
def __init__(self, date=None):
if date is None:
date = datetime.datetime.utcnow()
DateTime.__init__(self, date)
def storeOrUpdateAutoProcScalingStatistics(
self, _clientToolsForAutoprocessingWebService,
_xsDataAutoProcScalingStatistics):
"""Creates an entry in the ISPyB AutoProcScalingStatistics table"""
iAutoProcScalingStatisticsId = self.getXSValue(
_xsDataAutoProcScalingStatistics.getAutoProcScalingStatisticsId())
strScalingStatisticsType = self.getXSValue(
_xsDataAutoProcScalingStatistics.getScalingStatisticsType())
strComments = self.getXSValue(
_xsDataAutoProcScalingStatistics.getComments())
fResolutionLimitLow = self.getXSValue(
_xsDataAutoProcScalingStatistics.getResolutionLimitLow())
fResolutionLimitHigh = self.getXSValue(
_xsDataAutoProcScalingStatistics.getResolutionLimitHigh())
fRmerge = self.getXSValue(_xsDataAutoProcScalingStatistics.getRMerge())
fRmeasWithinIplusIminus = self.getXSValue(
_xsDataAutoProcScalingStatistics.getRmeasWithinIplusIminus())
fRmeasAllIplusIminus = self.getXSValue(
_xsDataAutoProcScalingStatistics.getRmeasAllIplusIminus())
fRpimWithinIplusIminus = self.getXSValue(
_xsDataAutoProcScalingStatistics.getRpimWithinIplusIminus())
fRpimAllIplusIminus = self.getXSValue(
_xsDataAutoProcScalingStatistics.getRpimAllIplusIminus())
fFractionalPartialBias = self.getXSValue(
_xsDataAutoProcScalingStatistics.getFractionalPartialBias())
iNtotalObservations = self.getXSValue(
_xsDataAutoProcScalingStatistics.getNTotalObservations())
iNtotalUniqueObservations = self.getXSValue(
_xsDataAutoProcScalingStatistics.getNtotalUniqueObservations())
fMeanIoverSigI = self.getXSValue(
_xsDataAutoProcScalingStatistics.getMeanIOverSigI())
fCompleteness = self.getXSValue(
_xsDataAutoProcScalingStatistics.getCompleteness())
fMultiplicity = self.getXSValue(
_xsDataAutoProcScalingStatistics.getMultiplicity())
fAnomalousCompleteness = self.getXSValue(
_xsDataAutoProcScalingStatistics.getAnomalousCompleteness())
fAnomalousMultiplicity = self.getXSValue(
_xsDataAutoProcScalingStatistics.getAnomalousMultiplicity())
recordTimeStamp = DateTime(datetime.datetime.now())
bAnomalous = self.getXSValue(
_xsDataAutoProcScalingStatistics.getAnomalous(), False)
iAutoProcScalingId = self.iAutoProcScalingId
fCcHalf = self.getXSValue(_xsDataAutoProcScalingStatistics.getCcHalf())
iAutoProcScalingStatisticsId = _clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProcScalingStatistics(
arg0=iAutoProcScalingStatisticsId, \
scalingStatisticsType=strScalingStatisticsType, \
comments=strComments, \
resolutionLimitLow=fResolutionLimitLow, \
resolutionLimitHigh=fResolutionLimitHigh, \
rmerge=fRmerge, \
rmeasWithinIplusIminus=fRmeasWithinIplusIminus, \
rmeasAllIplusIminus=fRmeasAllIplusIminus, \
rpimWithinIplusIminus=fRpimWithinIplusIminus, \
rpimAllIplusIminus=fRpimAllIplusIminus, \
fractionalPartialBias=fFractionalPartialBias, \
nTotalObservations=iNtotalObservations, \
nTotalUniqueObservations=iNtotalUniqueObservations, \
meanIoverSigI=fMeanIoverSigI, \
completeness=fCompleteness, \
multiplicity=fMultiplicity, \
anomalousCompleteness=fAnomalousCompleteness, \
anomalousMultiplicity=fAnomalousMultiplicity, \
recordTimeStamp=recordTimeStamp, \
anomalous=bAnomalous, \
autoProcScalingId=iAutoProcScalingId, \
ccHalf=fCcHalf, \
)
self.DEBUG("AutoProcScalingStatisticsId: %r" %
iAutoProcScalingStatisticsId)
return iAutoProcScalingStatisticsId
def storeOrUpdateAutoProcIntegration(
self, _clientToolsForAutoprocessingWebService,
_xsDataAutoProcIntegrationContainer):
"""Creates an entry in the ISPyB AutoProcIntegration table"""
xsDataProcIntegration = _xsDataAutoProcIntegrationContainer.getAutoProcIntegration(
)
iAutoProcIntegrationId = self.getXSValue(
xsDataProcIntegration.getAutoProcIntegrationId())
iAutoProcProgramId = self.iAutoProcProgramId
iStartImageNumber = self.getXSValue(
xsDataProcIntegration.getStartImageNumber())
iEndImageNumber = self.getXSValue(
xsDataProcIntegration.getEndImageNumber())
fRefinedDetectorDistance = self.getXSValue(
xsDataProcIntegration.getRefinedDetectorDistance())
fRefinedXbeam = self.getXSValue(
xsDataProcIntegration.getRefinedXbeam())
fRefinedYbeam = self.getXSValue(
xsDataProcIntegration.getRefinedYbeam())
fRotationAxisX = self.getXSValue(
xsDataProcIntegration.getRotationAxisX())
fRotationAxisY = self.getXSValue(
xsDataProcIntegration.getRotationAxisY())
fRotationAxisZ = self.getXSValue(
xsDataProcIntegration.getRotationAxisZ())
fBeamVectorX = self.getXSValue(xsDataProcIntegration.getBeamVectorX())
fBeamVectorY = self.getXSValue(xsDataProcIntegration.getBeamVectorY())
fBeamVectorZ = self.getXSValue(xsDataProcIntegration.getBeamVectorZ())
fCellA = self.getXSValue(xsDataProcIntegration.getCell_a())
fCellB = self.getXSValue(xsDataProcIntegration.getCell_b())
fCellC = self.getXSValue(xsDataProcIntegration.getCell_c())
fCellAlpha = self.getXSValue(xsDataProcIntegration.getCell_alpha())
fCellBeta = self.getXSValue(xsDataProcIntegration.getCell_beta())
fCellGamma = self.getXSValue(xsDataProcIntegration.getCell_gamma())
bAnomalous = self.getXSValue(xsDataProcIntegration.getAnomalous(),
False)
iDataCollectionId = _xsDataAutoProcIntegrationContainer.getImage(
).getDataCollectionId()
recordTimeStamp = DateTime(datetime.datetime.now())
iAutoProcIntegrationId = _clientToolsForAutoprocessingWebService.service.storeOrUpdateAutoProcIntegration(
arg0=iAutoProcIntegrationId, \
autoProcProgramId=iAutoProcProgramId, \
startImageNumber=iStartImageNumber, \
endImageNumber=iEndImageNumber, \
refinedDetectorDistance=fRefinedDetectorDistance, \
refinedXbeam=fRefinedXbeam, \
refinedYbeam=fRefinedYbeam, \
rotationAxisX=fRotationAxisX, \
rotationAxisY=fRotationAxisY, \
rotationAxisZ=fRotationAxisZ, \
beamVectorX=fBeamVectorX, \
beamVectorY=fBeamVectorY, \
beamVectorZ=fBeamVectorZ, \
cellA=fCellA, \
cellB=fCellB, \
cellC=fCellC, \
cellAlpha=fCellAlpha, \
cellBeta=fCellBeta, \
cellGamma=fCellGamma, \
recordTimeStamp=recordTimeStamp, \
anomalous=bAnomalous, \
dataCollectionId=iDataCollectionId \
)
self.DEBUG("AutoProcProgramIntegrationId: %r" % iAutoProcIntegrationId)
return iAutoProcIntegrationId
