def generateXSDataISPyBImage(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBImage
xsDataResultCharacterisationv2_0 = _xsDataInputControlISPyB.getCharacterisationResult()
xsDataResultCharacterisation = xsDataResultCharacterisationv2_0.getMxv1ResultCharacterisation()
xsDataISPyBImage = None
# Find path to first image from data collection information
strPathToFirstImage = None
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
lXSDataSubWedge = xsDataCollection.getSubWedge()
if (lXSDataSubWedge is not None):
xsDataSubWedgeFirst = lXSDataSubWedge[0]
lXSDataImage = xsDataSubWedgeFirst.getImage()
if (lXSDataImage is not None):
xsDataImageFirst = lXSDataImage[ 0 ]
strPathToFirstImage = xsDataImageFirst.getPath().getValue()
# Add an image path if the dataCollectionId is not present...
if (strPathToFirstImage is not None):
xsDataISPyBImage = XSDataISPyBImage()
strImageBaseName = EDUtilsFile.getBaseName(strPathToFirstImage)
strDirectoryName = EDUtilsPath.getFolderName(strPathToFirstImage)
xsDataISPyBImage.setFileName(XSDataString(strImageBaseName))
xsDataISPyBImage.setFileLocation(XSDataString(strDirectoryName))
return xsDataISPyBImage
def generateXSDataISPyBImage(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataString
from XSDataISPyBv1_2 import XSDataISPyBImage
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult(
)
xsDataISPyBImage = None
# Find path to first image from data collection information
strPathToFirstImage = None
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
lXSDataSubWedge = xsDataCollection.getSubWedge()
if (lXSDataSubWedge is not None):
xsDataSubWedgeFirst = lXSDataSubWedge[0]
lXSDataImage = xsDataSubWedgeFirst.getImage()
if (lXSDataImage is not None):
xsDataImageFirst = lXSDataImage[0]
strPathToFirstImage = xsDataImageFirst.getPath().getValue()
# Add an image path if the dataCollectionId is not present...
if (strPathToFirstImage is not None):
xsDataISPyBImage = XSDataISPyBImage()
strImageBaseName = EDUtilsFile.getBaseName(strPathToFirstImage)
strDirectoryName = EDUtilsPath.getFolderName(
strPathToFirstImage)
xsDataISPyBImage.setFileName(XSDataString(strImageBaseName))
xsDataISPyBImage.setFileLocation(
XSDataString(strDirectoryName))
return xsDataISPyBImage
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 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)