def process(self, _edObject=None):
"""
Sends store requests with the screening objects to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput("inputISPyB")[0] will be stored.
* Primary key attributes should not be set.
* If a foreign key attribute is not set, this method will attempt to find the foreign object among the
input objects, and then use the primary key attribute of this object when it has been stored. If such
an object is not found, the method fails.
* If an error is encountered, the method will immediately fail and will not attempt to store any more
objects.
"""
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.process")
# Basic sanity check of inputs:
if (self.hasDataInput("screening")):
if (len(self.getDataInput("screening")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", "There should only be one input 'screening'.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if (self.hasDataInput("screeningRankSet")):
if (len(self.getDataInput("screeningRankSet")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", "There should only be one input 'screeningRankSet'.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Get the inputs
xsDataISPyBScreenings = None
xsDataISPyBScreeningInputs = None
xsDataISPyBScreeningOutputContainers = None
xsDataISPyBScreeningRanks = None
xsDataISPyBScreeningRankSets = None
xsDataISPyBImages = None
xsDataISPyBScreeningFiles = None
if self.hasDataInput("screening"):
xsDataISPyBScreenings = self.getDataInput("screening")
if self.hasDataInput("screeningInput"):
xsDataISPyBScreeningInputs = self.getDataInput("screeningInput")
if self.hasDataInput("screeningOutputContainer"):
xsDataISPyBScreeningOutputContainers = self.getDataInput("screeningOutputContainer")
if self.hasDataInput("screeningRank"):
xsDataISPyBScreeningRanks = self.getDataInput("screeningRank")
if self.hasDataInput("screeningRankSet"):
xsDataISPyBScreeningRankSets = self.getDataInput("screeningRankSet")
if self.hasDataInput("image"):
xsDataISPyBImages = self.getDataInput("image")
if self.hasDataInput("screeningFile"):
xsDataISPyBScreeningFiles = self.getDataInput("screeningFile")
self.__xsDataResultISPyB = XSDataResultISPyB()
if (xsDataISPyBScreenings is None):
xsDataISPyBScreening = XSDataISPyBScreening()
else:
xsDataISPyBScreening = xsDataISPyBScreenings[0]
if (xsDataISPyBImages is None):
xsDataISPyBImage = None
else:
xsDataISPyBImage = xsDataISPyBImages[0]
# Another sanity check:
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None) or (xsDataISPyBImage.getFileName() == None) or (xsDataISPyBImage.getFileLocation() == None)):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", \
"Neither a dataCollectionId nor an image filename + path are provided.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
strResponse = self.httpPost(self.getDbserverHost(), self.getDbserverPort(), "/get_datacollectionid", strXML)
if strResponse != None:
# Handle response:
xsDatadbstatus = XSDatadbstatus.parseString(strResponse)
strCode = xsDatadbstatus.getCode()
strMessage = xsDatadbstatus.getMessage()
EDVerbose.DEBUG("dbserver returns code: " + strCode)
EDVerbose.DEBUG("dbserver returns message: " + strMessage)
if (strCode == "error") or (xsDatadbstatus.getDataCollectionId() == -1):
if xsDatadbstatus.getDataCollectionId() == -1:
strMessage = "An image corresponding to the given fileName and fileLocation was not found."
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", strMessage)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(XSDataInteger(xsDatadbstatus.getDataCollectionId()))
self.__xsDataResultISPyB.setDataCollectionId(XSDataInteger(xsDatadbstatus.getDataCollectionId()))
if (xsDataISPyBScreeningRankSets is None):
xsDataISPyBScreeningRankSet = None
else:
xsDataISPyBScreeningRankSet = xsDataISPyBScreeningRankSets[0]
# Store all the different screening* objects:
xsDataIntegerScreeningId = self.store(xsDataISPyBScreening)
if xsDataISPyBScreeningInputs != None:
for xsDataISPyBScreeningInput in xsDataISPyBScreeningInputs:
xsDataISPyBScreeningInput.setScreeningId(xsDataIntegerScreeningId)
self.store(xsDataISPyBScreeningInput)
if xsDataISPyBScreeningRankSet != None:
xsDataIntegerScreeningRankSetId = self.store(xsDataISPyBScreeningRankSet)
for xsDataISPyBScreeningRank in xsDataISPyBScreeningRanks:
xsDataISPyBScreeningRank.setScreeningId(xsDataIntegerScreeningId)
xsDataISPyBScreeningRank.setScreeningRankSetId(xsDataIntegerScreeningRankSetId)
self.store(xsDataISPyBScreeningRank)
if xsDataISPyBScreeningOutputContainers != None:
for xsDataISPyBScreeningOutputContainer in xsDataISPyBScreeningOutputContainers:
xsDataISPyBScreeningOutput = xsDataISPyBScreeningOutputContainer.getScreeningOutput()
xsDataISPyBScreeningOutput.setScreeningId(xsDataIntegerScreeningId)
xsDataIntegerScreeningOutputId = self.store(xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputLattices = xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice()
if xsDataISPyBScreeningOutputLattices != None:
for xsDataISPyBScreeningOutputLattice in xsDataISPyBScreeningOutputLattices:
xsDataISPyBScreeningOutputLattice.setScreeningOutputId(xsDataIntegerScreeningOutputId)
self.store(xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningStrategyContainers = xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer()
if xsDataISPyBScreeningStrategyContainers != None:
for xsDataISPyBScreeningStrategyContainer in xsDataISPyBScreeningStrategyContainers:
xsDataISPyBScreeningStrategy = xsDataISPyBScreeningStrategyContainer.getScreeningStrategy()
if xsDataISPyBScreeningStrategy != None:
xsDataISPyBScreeningStrategy.setScreeningOutputId(xsDataIntegerScreeningOutputId)
xsDataIntegerScreeningStrategyId = self.store(xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningStrategyWedgeContainers = xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer()
if xsDataISPyBScreeningStrategyWedgeContainers != None:
for xsDataISPyBScreeningStrategyWedgeContainer in xsDataISPyBScreeningStrategyWedgeContainers:
xsDataISPyBScreeningStrategyWedge = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategyWedge()
xsDataISPyBScreeningStrategyWedge.setScreeningStrategyId(xsDataIntegerScreeningStrategyId)
xsDataIntegerScreeningStrategyWedgeId = self.store(xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategySubWedges = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge()
if xsDataISPyBScreeningStrategySubWedges != None:
for xsDataISPyBScreeningStrategySubWedge in xsDataISPyBScreeningStrategySubWedges:
xsDataISPyBScreeningStrategySubWedge.setScreeningStrategyWedgeId(xsDataIntegerScreeningStrategyWedgeId)
self.store(xsDataISPyBScreeningStrategySubWedge)
def testSetDataModelInput(self):
"""
A test for whether we can obtain the expected XML by setting a certain input for the plugin.
"""
edPluginISPyB = self.createPlugin()
xsPluginItemISPyB = self.getPluginConfiguration(os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
edPluginISPyB.setConfiguration(xsPluginItemISPyB)
edPluginISPyB.configure()
# Create XSDataISPyB objects
xsDataISPyBImage = XSDataISPyBImage()
xsDataISPyBImage.setFileName(XSDataString("test.img"))
xsDataISPyBImage.setFileLocation(XSDataString("/tmp"))
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA Prototype"))
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
xsDataISPyBScreeningInput.setBeamX(XSDataDouble(10.4))
xsDataISPyBScreeningInput.setBeamY(XSDataDouble(2.31))
xsDataISPyBScreeningInput.setRmsErrorLimits(XSDataDouble(0.8))
xsDataISPyBScreeningInput.setMinimumFractionIndexed(XSDataDouble(0.4))
xsDataISPyBScreeningInput.setMaximumFractionRejected(XSDataDouble(0.45))
xsDataISPyBScreeningInput.setMinimumSignalToNoise(XSDataDouble(0.56))
xsDataISPyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutput.setStatusDescription(XSDataString("It's just fine."))
xsDataISPyBScreeningOutput.setMosaicity(XSDataDouble(0.25))
xsDataISPyBScreeningOutput.setBeamShiftX(XSDataDouble (0.141))
xsDataISPyBScreeningOutput.setBeamShiftY(XSDataDouble (0.156))
xsDataISPyBScreeningOutputLattice = XSDataISPyBScreeningOutputLattice()
xsDataISPyBScreeningOutputLattice.setSpaceGroup(XSDataString("P222"))
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
xsDataISPyBScreeningStrategy.setPhiStart(XSDataDouble(0))
xsDataISPyBScreeningStrategy.setPhiEnd(XSDataDouble(20))
xsDataISPyBScreeningStrategy.setRotation(XSDataDouble(1))
xsDataISPyBScreeningStrategy.setProgram(XSDataString("EDNA"))
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(1))
xsDataISPyBScreeningStrategyWedge = XSDataISPyBScreeningStrategyWedge()
xsDataISPyBScreeningStrategyWedge.setWedgeNumber(XSDataInteger(1))
xsDataISPyBScreeningStrategyWedge.setResolution(XSDataDouble(2.1))
xsDataISPyBScreeningStrategyWedge.setCompleteness(XSDataDouble(90))
xsDataISPyBScreeningStrategyWedge.setMultiplicity(XSDataDouble(1.5))
xsDataISPyBScreeningStrategyWedge.setDoseTotal(XSDataDouble(40.5))
xsDataISPyBScreeningStrategyWedge.setNumberOfImages(XSDataInteger(130))
xsDataISPyBScreeningStrategySubWedge = XSDataISPyBScreeningStrategySubWedge()
xsDataISPyBScreeningStrategySubWedge.setSubWedgeNumber(XSDataInteger(1))
xsDataISPyBScreeningStrategySubWedge.setRotationAxis(XSDataString("Omega"))
xsDataISPyBScreeningStrategySubWedge.setAxisStart(XSDataDouble(0.0))
xsDataISPyBScreeningStrategySubWedge.setAxisEnd(XSDataDouble(90.0))
xsDataISPyBScreeningStrategySubWedge.setExposureTime(XSDataDouble(0.5))
xsDataISPyBScreeningStrategySubWedge.setTransmission(XSDataDouble(100.0))
xsDataISPyBScreeningStrategySubWedge.setNumberOfImages(XSDataInteger(130))
xsDataISPyBScreeningStrategyWedgeContainer = XSDataISPyBScreeningStrategyWedgeContainer()
xsDataISPyBScreeningStrategyWedgeContainer.setScreeningStrategyWedge(xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge().append(xsDataISPyBScreeningStrategySubWedge)
xsDataISPyBScreeningStrategyContainer = XSDataISPyBScreeningStrategyContainer()
xsDataISPyBScreeningStrategyContainer.setScreeningStrategy(xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer().append(xsDataISPyBScreeningStrategyWedgeContainer)
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer()
xsDataISPyBScreeningOutputContainer.setScreeningOutput(xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice().append(xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer().append(xsDataISPyBScreeningStrategyContainer)
xsDataISPyBScreeningRank = XSDataISPyBScreeningRank()
xsDataISPyBScreeningRank.setRankValue(XSDataDouble(1.4))
xsDataISPyBScreeningRank.setRankInformation(XSDataString("This is the only one"))
xsDataISPyBScreeningRankSet = XSDataISPyBScreeningRankSet()
xsDataISPyBScreeningRankSet.setRankEngine(XSDataString("ISPyB"))
xsDataISPyBScreeningFile = XSDataISPyBScreeningFile()
xsDataISPyBScreeningFile.setFileType(XSDataString("log"))
xsDataISPyBScreeningFile.setDescription(XSDataString("Output log file"))
# Write XSDataISPyB objects to files
xsDataISPyBScreening.outputFile(self.__strObtainedScreening)
xsDataISPyBScreeningInput.outputFile(self.__strObtainedScreeningInput)
xsDataISPyBScreeningOutputContainer.outputFile(self.__strObtainedScreeningOutputContainer)
xsDataISPyBScreeningRank.outputFile(self.__strObtainedScreeningRank)
xsDataISPyBScreeningRankSet.outputFile(self.__strObtainedScreeningRankSet)
xsDataISPyBScreeningFile.outputFile(self.__strObtainedScreeningFile)
# Compare screening
strInputScreeningExpected = self.readAndParseFile(self.__strReferenceInputScreening)
xsDataScreeningExpected = XSDataInputISPyB.parseString(strInputScreeningExpected)
strXMLScreeningExpected = xsDataScreeningExpected.marshal()
strScreeningObtained = self.readAndParseFile(self.__strObtainedScreening)
xsDataScreeningObtained = XSDataInputISPyB.parseString(strScreeningObtained)
strXMLScreeningObtained = xsDataScreeningObtained.marshal()
EDAssert.equal(strXMLScreeningExpected, strXMLScreeningObtained)
#Compare screeningInput
strInputScreeningInputExpected = self.readAndParseFile(self.__strReferenceInputScreeningInput)
xsDataScreeningInputExpected = XSDataInputISPyB.parseString(strInputScreeningInputExpected)
strXMLScreeningInputExpected = xsDataScreeningInputExpected.marshal()
strScreeningInputObtained = self.readAndParseFile(self.__strObtainedScreeningInput)
xsDataScreeningInputObtained = XSDataInputISPyB.parseString(strScreeningInputObtained)
strXMLScreeningInputObtained = xsDataScreeningInputObtained.marshal()
EDAssert.equal(strXMLScreeningInputExpected, strXMLScreeningInputObtained)
#Compare screeningOutputContainer
strInputScreeningOutputContainerExpected = self.readAndParseFile(self.__strReferenceInputScreeningOutputContainer)
xsDataScreeningOutputContainerExpected = XSDataInputISPyB.parseString(strInputScreeningOutputContainerExpected)
strXMLScreeningOutputContainerExpected = xsDataScreeningOutputContainerExpected.marshal()
strScreeningOutputContainerObtained = self.readAndParseFile(self.__strObtainedScreeningOutputContainer)
xsDataScreeningOutputContainerObtained = XSDataInputISPyB.parseString(strScreeningOutputContainerObtained)
strXMLScreeningOutputContainerObtained = xsDataScreeningOutputContainerObtained.marshal()
EDAssert.equal(strXMLScreeningOutputContainerExpected, strXMLScreeningOutputContainerObtained)
#Compare screeningRank
strInputScreeningRankExpected = self.readAndParseFile(self.__strReferenceInputScreeningRank)
xsDataScreeningRankExpected = XSDataInputISPyB.parseString(strInputScreeningRankExpected)
strXMLScreeningRankExpected = xsDataScreeningRankExpected.marshal()
strScreeningRankObtained = self.readAndParseFile(self.__strObtainedScreeningRank)
xsDataScreeningRankObtained = XSDataInputISPyB.parseString(strScreeningRankObtained)
strXMLScreeningRankObtained = xsDataScreeningRankObtained.marshal()
EDAssert.equal(strXMLScreeningRankExpected, strXMLScreeningRankObtained)
#Compare screeningRankSet
strInputScreeningRankSetExpected = self.readAndParseFile(self.__strReferenceInputScreeningRankSet)
xsDataScreeningRankSetExpected = XSDataInputISPyB.parseString(strInputScreeningRankSetExpected)
strXMLScreeningRankSetExpected = xsDataScreeningRankSetExpected.marshal()
strScreeningRankSetObtained = self.readAndParseFile(self.__strObtainedScreeningRankSet)
xsDataScreeningRankSetObtained = XSDataInputISPyB.parseString(strScreeningRankSetObtained)
strXMLScreeningRankSetObtained = xsDataScreeningRankSetObtained.marshal()
EDAssert.equal(strXMLScreeningRankSetExpected, strXMLScreeningRankSetObtained)
#Compare screeningFile
strInputScreeningFileExpected = self.readAndParseFile(self.__strReferenceInputScreeningFile)
xsDataScreeningFileExpected = XSDataInputISPyB.parseString(strInputScreeningFileExpected)
strXMLScreeningFileExpected = xsDataScreeningFileExpected.marshal()
strScreeningFileObtained = self.readAndParseFile(self.__strObtainedScreeningFile)
xsDataScreeningFileObtained = XSDataInputISPyB.parseString(strScreeningFileObtained)
strXMLScreeningFileObtained = xsDataScreeningFileObtained.marshal()
EDAssert.equal(strXMLScreeningFileExpected, strXMLScreeningFileObtained)
self.cleanUp(edPluginISPyB)
def generateXSDataISPyBScreening(_xsDataInputControlISPyB,
_strShortComments=None,
_strComments=None):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBScreening
xsDataIntegerDataCollectionId = _xsDataInputControlISPyB.getDataCollectionId(
)
# General information
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA MXv1"))
pyStrTimeStamp = time.strftime("%Y-%m-%d %H:%M:%S")
xsDataISPyBScreening.setTimeStamp(XSDataString(pyStrTimeStamp))
if (not _strShortComments is None):
xsDataISPyBScreening.setShortComments(
XSDataString(_strShortComments))
if (not _strComments is None):
xsDataISPyBScreening.setComments(XSDataString(_strComments))
# Use dataCollectionId if provided in the input
if (xsDataIntegerDataCollectionId is not None):
xsDataISPyBScreening.setDataCollectionId(
xsDataIntegerDataCollectionId)
return xsDataISPyBScreening
def generateXSDataISPyBScreening(_xsDataInputControlISPyB, _strShortComments=None, _strComments=None):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBScreening
xsDataIntegerDataCollectionId = _xsDataInputControlISPyB.getDataCollectionId()
# General information
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA MXv1"))
pyStrTimeStamp = time.strftime("%Y-%m-%d %H:%M:%S")
xsDataISPyBScreening.setTimeStamp(XSDataString(pyStrTimeStamp))
if (not _strShortComments is None):
xsDataISPyBScreening.setShortComments(XSDataString(_strShortComments))
if (not _strComments is None):
xsDataISPyBScreening.setComments(XSDataString(_strComments))
# Use dataCollectionId if provided in the input
if (xsDataIntegerDataCollectionId is not None):
xsDataISPyBScreening.setDataCollectionId(xsDataIntegerDataCollectionId)
return xsDataISPyBScreening
def testSetDataModelInput(self):
"""
A test for whether we can obtain the expected XML by setting a certain input for the plugin.
"""
edPluginISPyB = self.createPlugin()
xsPluginItemISPyB = self.getPluginConfiguration(
os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
edPluginISPyB.setConfiguration(xsPluginItemISPyB)
edPluginISPyB.configure()
# Create XSDataISPyB objects
xsDataISPyBImage = XSDataISPyBImage()
xsDataISPyBImage.setFileName(XSDataString("test.img"))
xsDataISPyBImage.setFileLocation(XSDataString("/tmp"))
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBScreening.setProgramVersion(XSDataString("EDNA Prototype"))
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
xsDataISPyBScreeningInput.setBeamX(XSDataDouble(10.4))
xsDataISPyBScreeningInput.setBeamY(XSDataDouble(2.31))
xsDataISPyBScreeningInput.setRmsErrorLimits(XSDataDouble(0.8))
xsDataISPyBScreeningInput.setMinimumFractionIndexed(XSDataDouble(0.4))
xsDataISPyBScreeningInput.setMaximumFractionRejected(
XSDataDouble(0.45))
xsDataISPyBScreeningInput.setMinimumSignalToNoise(XSDataDouble(0.56))
xsDataISPyBScreeningOutput = XSDataISPyBScreeningOutput()
xsDataISPyBScreeningOutput.setStatusDescription(
XSDataString("It's just fine."))
xsDataISPyBScreeningOutput.setMosaicity(XSDataDouble(0.25))
xsDataISPyBScreeningOutput.setBeamShiftX(XSDataDouble(0.141))
xsDataISPyBScreeningOutput.setBeamShiftY(XSDataDouble(0.156))
xsDataISPyBScreeningOutputLattice = XSDataISPyBScreeningOutputLattice()
xsDataISPyBScreeningOutputLattice.setSpaceGroup(XSDataString("P222"))
xsDataISPyBScreeningStrategy = XSDataISPyBScreeningStrategy()
xsDataISPyBScreeningStrategy.setPhiStart(XSDataDouble(0))
xsDataISPyBScreeningStrategy.setPhiEnd(XSDataDouble(20))
xsDataISPyBScreeningStrategy.setRotation(XSDataDouble(1))
xsDataISPyBScreeningStrategy.setProgram(XSDataString("EDNA"))
xsDataISPyBScreeningStrategy.setAnomalous(XSDataBoolean(1))
xsDataISPyBScreeningStrategyWedge = XSDataISPyBScreeningStrategyWedge()
xsDataISPyBScreeningStrategyWedge.setWedgeNumber(XSDataInteger(1))
xsDataISPyBScreeningStrategyWedge.setResolution(XSDataDouble(2.1))
xsDataISPyBScreeningStrategyWedge.setCompleteness(XSDataDouble(90))
xsDataISPyBScreeningStrategyWedge.setMultiplicity(XSDataDouble(1.5))
xsDataISPyBScreeningStrategyWedge.setDoseTotal(XSDataDouble(40.5))
xsDataISPyBScreeningStrategyWedge.setNumberOfImages(XSDataInteger(130))
xsDataISPyBScreeningStrategySubWedge = XSDataISPyBScreeningStrategySubWedge(
)
xsDataISPyBScreeningStrategySubWedge.setSubWedgeNumber(
XSDataInteger(1))
xsDataISPyBScreeningStrategySubWedge.setRotationAxis(
XSDataString("Omega"))
xsDataISPyBScreeningStrategySubWedge.setAxisStart(XSDataDouble(0.0))
xsDataISPyBScreeningStrategySubWedge.setAxisEnd(XSDataDouble(90.0))
xsDataISPyBScreeningStrategySubWedge.setExposureTime(XSDataDouble(0.5))
xsDataISPyBScreeningStrategySubWedge.setTransmission(
XSDataDouble(100.0))
xsDataISPyBScreeningStrategySubWedge.setNumberOfImages(
XSDataInteger(130))
xsDataISPyBScreeningStrategyWedgeContainer = XSDataISPyBScreeningStrategyWedgeContainer(
)
xsDataISPyBScreeningStrategyWedgeContainer.setScreeningStrategyWedge(
xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge(
).append(xsDataISPyBScreeningStrategySubWedge)
xsDataISPyBScreeningStrategyContainer = XSDataISPyBScreeningStrategyContainer(
)
xsDataISPyBScreeningStrategyContainer.setScreeningStrategy(
xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer(
).append(xsDataISPyBScreeningStrategyWedgeContainer)
xsDataISPyBScreeningOutputContainer = XSDataISPyBScreeningOutputContainer(
)
xsDataISPyBScreeningOutputContainer.setScreeningOutput(
xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice().append(
xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer(
).append(xsDataISPyBScreeningStrategyContainer)
xsDataISPyBScreeningRank = XSDataISPyBScreeningRank()
xsDataISPyBScreeningRank.setRankValue(XSDataDouble(1.4))
xsDataISPyBScreeningRank.setRankInformation(
XSDataString("This is the only one"))
xsDataISPyBScreeningRankSet = XSDataISPyBScreeningRankSet()
xsDataISPyBScreeningRankSet.setRankEngine(XSDataString("ISPyB"))
xsDataISPyBScreeningFile = XSDataISPyBScreeningFile()
xsDataISPyBScreeningFile.setFileType(XSDataString("log"))
xsDataISPyBScreeningFile.setDescription(
XSDataString("Output log file"))
# Write XSDataISPyB objects to files
xsDataISPyBScreening.outputFile(self.__strObtainedScreening)
xsDataISPyBScreeningInput.outputFile(self.__strObtainedScreeningInput)
xsDataISPyBScreeningOutputContainer.outputFile(
self.__strObtainedScreeningOutputContainer)
xsDataISPyBScreeningRank.outputFile(self.__strObtainedScreeningRank)
xsDataISPyBScreeningRankSet.outputFile(
self.__strObtainedScreeningRankSet)
xsDataISPyBScreeningFile.outputFile(self.__strObtainedScreeningFile)
# Compare screening
strInputScreeningExpected = self.readAndParseFile(
self.__strReferenceInputScreening)
xsDataScreeningExpected = XSDataInputISPyB.parseString(
strInputScreeningExpected)
strXMLScreeningExpected = xsDataScreeningExpected.marshal()
strScreeningObtained = self.readAndParseFile(
self.__strObtainedScreening)
xsDataScreeningObtained = XSDataInputISPyB.parseString(
strScreeningObtained)
strXMLScreeningObtained = xsDataScreeningObtained.marshal()
EDAssert.equal(strXMLScreeningExpected, strXMLScreeningObtained)
#Compare screeningInput
strInputScreeningInputExpected = self.readAndParseFile(
self.__strReferenceInputScreeningInput)
xsDataScreeningInputExpected = XSDataInputISPyB.parseString(
strInputScreeningInputExpected)
strXMLScreeningInputExpected = xsDataScreeningInputExpected.marshal()
strScreeningInputObtained = self.readAndParseFile(
self.__strObtainedScreeningInput)
xsDataScreeningInputObtained = XSDataInputISPyB.parseString(
strScreeningInputObtained)
strXMLScreeningInputObtained = xsDataScreeningInputObtained.marshal()
EDAssert.equal(strXMLScreeningInputExpected,
strXMLScreeningInputObtained)
#Compare screeningOutputContainer
strInputScreeningOutputContainerExpected = self.readAndParseFile(
self.__strReferenceInputScreeningOutputContainer)
xsDataScreeningOutputContainerExpected = XSDataInputISPyB.parseString(
strInputScreeningOutputContainerExpected)
strXMLScreeningOutputContainerExpected = xsDataScreeningOutputContainerExpected.marshal(
)
strScreeningOutputContainerObtained = self.readAndParseFile(
self.__strObtainedScreeningOutputContainer)
xsDataScreeningOutputContainerObtained = XSDataInputISPyB.parseString(
strScreeningOutputContainerObtained)
strXMLScreeningOutputContainerObtained = xsDataScreeningOutputContainerObtained.marshal(
)
EDAssert.equal(strXMLScreeningOutputContainerExpected,
strXMLScreeningOutputContainerObtained)
#Compare screeningRank
strInputScreeningRankExpected = self.readAndParseFile(
self.__strReferenceInputScreeningRank)
xsDataScreeningRankExpected = XSDataInputISPyB.parseString(
strInputScreeningRankExpected)
strXMLScreeningRankExpected = xsDataScreeningRankExpected.marshal()
strScreeningRankObtained = self.readAndParseFile(
self.__strObtainedScreeningRank)
xsDataScreeningRankObtained = XSDataInputISPyB.parseString(
strScreeningRankObtained)
strXMLScreeningRankObtained = xsDataScreeningRankObtained.marshal()
EDAssert.equal(strXMLScreeningRankExpected,
strXMLScreeningRankObtained)
#Compare screeningRankSet
strInputScreeningRankSetExpected = self.readAndParseFile(
self.__strReferenceInputScreeningRankSet)
xsDataScreeningRankSetExpected = XSDataInputISPyB.parseString(
strInputScreeningRankSetExpected)
strXMLScreeningRankSetExpected = xsDataScreeningRankSetExpected.marshal(
)
strScreeningRankSetObtained = self.readAndParseFile(
self.__strObtainedScreeningRankSet)
xsDataScreeningRankSetObtained = XSDataInputISPyB.parseString(
strScreeningRankSetObtained)
strXMLScreeningRankSetObtained = xsDataScreeningRankSetObtained.marshal(
)
EDAssert.equal(strXMLScreeningRankSetExpected,
strXMLScreeningRankSetObtained)
#Compare screeningFile
strInputScreeningFileExpected = self.readAndParseFile(
self.__strReferenceInputScreeningFile)
xsDataScreeningFileExpected = XSDataInputISPyB.parseString(
strInputScreeningFileExpected)
strXMLScreeningFileExpected = xsDataScreeningFileExpected.marshal()
strScreeningFileObtained = self.readAndParseFile(
self.__strObtainedScreeningFile)
xsDataScreeningFileObtained = XSDataInputISPyB.parseString(
strScreeningFileObtained)
strXMLScreeningFileObtained = xsDataScreeningFileObtained.marshal()
EDAssert.equal(strXMLScreeningFileExpected,
strXMLScreeningFileObtained)
self.cleanUp(edPluginISPyB)
def process(self, _edObject=None):
"""
Sends store requests with the screening objects to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput("inputISPyB")[0] will be stored.
* Primary key attributes should not be set.
* If a foreign key attribute is not set, this method will attempt to find the foreign object among the
input objects, and then use the primary key attribute of this object when it has been stored. If such
an object is not found, the method fails.
* If an error is encountered, the method will immediately fail and will not attempt to store any more
objects.
"""
EDPluginExec.process(self)
self.DEBUG("*** EDPluginISPyBv1_2.process")
# Basic sanity check of inputs:
if (self.hasDataInput("screening")):
if (len(self.getDataInput("screening")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process",
"There should only be one input 'screening'.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if (self.hasDataInput("screeningRankSet")):
if (len(self.getDataInput("screeningRankSet")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process",
"There should only be one input 'screeningRankSet'.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Get the inputs
xsDataISPyBScreenings = None
xsDataISPyBScreeningInputs = None
xsDataISPyBScreeningOutputContainers = None
xsDataISPyBScreeningRanks = None
xsDataISPyBScreeningRankSets = None
xsDataISPyBImages = None
xsDataISPyBScreeningFiles = None
if self.hasDataInput("screening"):
xsDataISPyBScreenings = self.getDataInput("screening")
if self.hasDataInput("screeningInput"):
xsDataISPyBScreeningInputs = self.getDataInput("screeningInput")
if self.hasDataInput("screeningOutputContainer"):
xsDataISPyBScreeningOutputContainers = self.getDataInput(
"screeningOutputContainer")
if self.hasDataInput("screeningRank"):
xsDataISPyBScreeningRanks = self.getDataInput("screeningRank")
if self.hasDataInput("screeningRankSet"):
xsDataISPyBScreeningRankSets = self.getDataInput(
"screeningRankSet")
if self.hasDataInput("image"):
xsDataISPyBImages = self.getDataInput("image")
if self.hasDataInput("screeningFile"):
xsDataISPyBScreeningFiles = self.getDataInput("screeningFile")
self.__xsDataResultISPyB = XSDataResultISPyB()
if (xsDataISPyBScreenings is None):
xsDataISPyBScreening = XSDataISPyBScreening()
else:
xsDataISPyBScreening = xsDataISPyBScreenings[0]
if (xsDataISPyBImages is None):
xsDataISPyBImage = None
else:
xsDataISPyBImage = xsDataISPyBImages[0]
# Another sanity check:
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None)
or (xsDataISPyBImage.getFileName() == None)
or (xsDataISPyBImage.getFileLocation() == None)):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", \
"Neither a dataCollectionId nor an image filename + path are provided.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
strResponse = self.httpPost(self.getDbserverHost(),
self.getDbserverPort(),
"/get_datacollectionid", strXML)
if strResponse != None:
# Handle response:
xsDatadbstatus = XSDatadbstatus.parseString(strResponse)
strCode = xsDatadbstatus.getCode()
strMessage = xsDatadbstatus.getMessage()
self.DEBUG("dbserver returns code: " + strCode)
self.DEBUG("dbserver returns message: " + strMessage)
if (strCode
== "error") or (xsDatadbstatus.getDataCollectionId()
== -1):
if xsDatadbstatus.getDataCollectionId() == -1:
strMessage = "An image corresponding to the given fileName and fileLocation was not found."
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process", strMessage)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(
XSDataInteger(xsDatadbstatus.getDataCollectionId()))
self.__xsDataResultISPyB.setDataCollectionId(
XSDataInteger(xsDatadbstatus.getDataCollectionId()))
if (xsDataISPyBScreeningRankSets is None):
xsDataISPyBScreeningRankSet = None
else:
xsDataISPyBScreeningRankSet = xsDataISPyBScreeningRankSets[0]
# Store all the different screening* objects:
xsDataIntegerScreeningId = self.store(xsDataISPyBScreening)
if xsDataISPyBScreeningInputs != None:
for xsDataISPyBScreeningInput in xsDataISPyBScreeningInputs:
xsDataISPyBScreeningInput.setScreeningId(
xsDataIntegerScreeningId)
self.store(xsDataISPyBScreeningInput)
if xsDataISPyBScreeningRankSet != None:
xsDataIntegerScreeningRankSetId = self.store(
xsDataISPyBScreeningRankSet)
for xsDataISPyBScreeningRank in xsDataISPyBScreeningRanks:
xsDataISPyBScreeningRank.setScreeningId(
xsDataIntegerScreeningId)
xsDataISPyBScreeningRank.setScreeningRankSetId(
xsDataIntegerScreeningRankSetId)
self.store(xsDataISPyBScreeningRank)
if xsDataISPyBScreeningOutputContainers != None:
for xsDataISPyBScreeningOutputContainer in xsDataISPyBScreeningOutputContainers:
xsDataISPyBScreeningOutput = xsDataISPyBScreeningOutputContainer.getScreeningOutput(
)
xsDataISPyBScreeningOutput.setScreeningId(
xsDataIntegerScreeningId)
xsDataIntegerScreeningOutputId = self.store(
xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputLattices = xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice(
)
if xsDataISPyBScreeningOutputLattices != None:
for xsDataISPyBScreeningOutputLattice in xsDataISPyBScreeningOutputLattices:
xsDataISPyBScreeningOutputLattice.setScreeningOutputId(
xsDataIntegerScreeningOutputId)
self.store(xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningStrategyContainers = xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer(
)
if xsDataISPyBScreeningStrategyContainers != None:
for xsDataISPyBScreeningStrategyContainer in xsDataISPyBScreeningStrategyContainers:
xsDataISPyBScreeningStrategy = xsDataISPyBScreeningStrategyContainer.getScreeningStrategy(
)
if xsDataISPyBScreeningStrategy != None:
xsDataISPyBScreeningStrategy.setScreeningOutputId(
xsDataIntegerScreeningOutputId)
xsDataIntegerScreeningStrategyId = self.store(
xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningStrategyWedgeContainers = xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer(
)
if xsDataISPyBScreeningStrategyWedgeContainers != None:
for xsDataISPyBScreeningStrategyWedgeContainer in xsDataISPyBScreeningStrategyWedgeContainers:
xsDataISPyBScreeningStrategyWedge = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategyWedge(
)
xsDataISPyBScreeningStrategyWedge.setScreeningStrategyId(
xsDataIntegerScreeningStrategyId)
xsDataIntegerScreeningStrategyWedgeId = self.store(
xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategySubWedges = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge(
)
if xsDataISPyBScreeningStrategySubWedges != None:
for xsDataISPyBScreeningStrategySubWedge in xsDataISPyBScreeningStrategySubWedges:
xsDataISPyBScreeningStrategySubWedge.setScreeningStrategyWedgeId(
xsDataIntegerScreeningStrategyWedgeId
)
self.store(
xsDataISPyBScreeningStrategySubWedge
)