def preProcess(self, _edPlugin=None):
"""
This method prepares the input for the CCP4i plugin and loads it.
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.preProcess...")
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataInputCCP4i
xsDataInputCCP4i = XSDataInputCCP4i()
xsDataInputMXCuBE = self.getDataInput()
xsDataInputCCP4i.setDataSet(xsDataInputMXCuBE.getDataSet())
#xsDataInputCCP4i.setDataFile( xsDataInputMXCuBE.getDataFile() )
xsDataInputCCP4i.setExperimentalCondition(xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputCCP4i.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputCCP4i.setSample(xsDataInputMXCuBE.getSample())
self.__edPluginControlCCP4i = self.loadPlugin(self.__strPluginControlCCP4i, "CCP4i")
self.__edPluginControlCCP4i.setDataInput(xsDataInputCCP4i)
self.__xsDataIntegerDataCollectionId = xsDataInputMXCuBE.getDataCollectionId()
if (self.__xsDataIntegerDataCollectionId is not None):
self.__edPluginControlISPyB = self.loadPlugin(self.__strPluginControlISPyB, "ISPyB")
self.__edPluginExecOutputHTML = self.loadPlugin(self.__strPluginExecOutputHTMLName, "OutputHTML")
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 testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath,
strReferenceInputControlISPyBFile)
strXMLIndexingInput = self.readAndParseFile(strPath)
from XSDataMXv1 import XSDataInputControlISPyB
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(
strXMLIndexingInput)
from EDHandlerXSDataISPyBv1_1 import EDHandlerXSDataISPyBv1_1
xsDataInputISPyB = EDHandlerXSDataISPyBv1_1.generateXSDataInputISPyB(
xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath,
strReferenceInputISPyBFile)
strXMLInputISPyBReference = self.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataInputISPyB
xsDataInputISPyBReference = XSDataInputISPyB.parseString(
strXMLInputISPyBReference)
# Remove the time strings since they otherwise make the test fail
xsDataInputISPyBReference.getScreening().setTimeStamp(None)
xsDataInputISPyB.getScreening().setTimeStamp(None)
EDAssert.equal(xsDataInputISPyBReference.marshal(),
xsDataInputISPyB.marshal())
def writeKappaSettings(self):
'''
# future version for getting motor positions related to images under processing
# checking in order:
# - value got as input
# - mosflm.descr file in process subdir (if BCM (like mxcube) registered it)
# - {imageTemplate}_kappa_settings.xml file (if BCM (like DNA) registered it)
# - read it now (and try to register as {imageTemplate}_kappa_settings.xml)
# - just use the datum (0,0,0)
'''
#code for using a predefined datum (0;0;0)
#EDUtilsFile.writeFile( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "DNA_STAC_Kappa_Settings" ), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>0.000000</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>")
# gonio settings from DC descriptor object
EDFactoryPluginStatic.loadModule("XSDataMXv2")
#import XSDataMXv2
#dc = XSDataMXv2.XSDataCollection()
from XSDataMXv2 import XSDataCollection
dc = XSDataCollection()
dc = self.getDataInput("dataCollection")[0]
omega = dc.getXSSubWedge()[0].getXSRotationalGoniostatSetting(
).getBaseaxissetting()
[kappa, phi] = dc.getXSSubWedge()[0].getXSRotationalGoniostatSetting(
).getAxissetting()
EDUtilsFile.writeFile(
os.path.join(self.getWorkingDirectory(),
"DNA_STAC_Kappa_Settings"),
"<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>"
% (omega.getValue(), kappa.getValue(), phi.getValue()))
'''
def testGenerateXSDataInputBestv1_2(
self, _strFileNameXSDataInputStrategy_reference,
_strFileNameXSDataInputBest_reference):
"""
This method is testing the generation of the XSDataInputBest object given a XSDataIndexingStrategy object.
"""
strReferenceInputFile = os.path.join(
self.strDataPath, _strFileNameXSDataInputStrategy_reference)
strPath = os.path.join(self.strDataPath, strReferenceInputFile)
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategy = XSDataInputStrategy.parseFile(strPath)
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
edHandlerXSDataBestv1_2 = EDHandlerXSDataBestv1_2()
xsDataInputBestv1_2 = edHandlerXSDataBestv1_2.getXSDataInputBest(
xsDataInputStrategy)
strReferencePath = os.path.join(self.strDataPath,
_strFileNameXSDataInputBest_reference)
strXMLInputBestReference = EDUtilsTest.readAndParseFile(
strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBestReference = XSDataInputBest.parseString(
strXMLInputBestReference)
EDAssert.equal(xsDataInputBestReference.marshal(),
xsDataInputBestv1_2.marshal())
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 generateXSDataISPyBScreeningInput(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataISPyBScreeningInput
from XSDataISPyBv1_2 import XSDataDouble
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult(
)
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
# Data collection information
xsDataCollection = xsDataResultCharacterisation.getDataCollection()
if (xsDataCollection is not None):
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if (xsDataSubWedgeList is not None):
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataExperimentalCondition = xsDataSubWedgeFirst.getExperimentalCondition(
)
if (xsDataExperimentalCondition is not None):
xsDataDetector = xsDataExperimentalCondition.getDetector()
if (xsDataDetector is not None):
fBeamPositionX = xsDataDetector.getBeamPositionX(
).getValue()
fBeamPositionY = xsDataDetector.getBeamPositionY(
).getValue()
xsDataISPyBScreeningInput.setBeamX(
XSDataDouble(fBeamPositionX))
xsDataISPyBScreeningInput.setBeamY(
XSDataDouble(fBeamPositionY))
return xsDataISPyBScreeningInput
def mergeAtomicComposition(self, _xsDataAtomicComposition1, _xsDataAtomicComposition2):
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
mergedAtomicComposition = XSDataAtomicComposition()
dictionary = {}
for atom in _xsDataAtomicComposition2.getAtom():
dictionary[atom.getSymbol().getValue()] = atom.getNumberOf().getValue()
for atom1 in _xsDataAtomicComposition1.getAtom():
symbol = atom1.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition2) == True):
mergedAtom = XSDataAtom()
mergedAtom.setNumberOf(XSDataDouble(atom1.getNumberOf().getValue() + dictionary[symbol]))
mergedAtom.setSymbol(XSDataString(symbol))
mergedAtomicComposition.addAtom(mergedAtom)
else:
mergedAtomicComposition.addAtom(atom1)
for atom2 in _xsDataAtomicComposition2.getAtom():
symbol = atom2.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition1) == False):
mergedAtomicComposition.addAtom(atom2)
return mergedAtomicComposition
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
#self.setXSDataInputClass( XSDataInputCharacterisation )
#self.setXSDataInputClass(EDList)
#self.strPluginIndexingName = "EDPluginControlIndexingv2_0"
self.strPluginIndexingName = "EDPluginControlIndexingv10"
self.edPluginIndexing = None
self.strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.edPluginIntegration = None
self.strPluginStrategyName = "EDPluginControlKappaStrategyv2_0"
self.edPluginStrategy = None
self.xsDataResultCharacterisationv2_0 = None
self.xsDataResultCharacterisation = None
self.xsDataInputStrategy = None
self.setXSDataInputClass(XSDataInputCharacterisationv2_0)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataInputCharacterisation, "mxv1InputCharacterisation")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection, "mxv2DataCollection")
def writeKappaSettings(self):
'''
# future version for getting motor positions related to images under processing
# checking in order:
# - value got as input
# - mosflm.descr file in process subdir (if BCM (like mxcube) registered it)
# - {imageTemplate}_kappa_settings.xml file (if BCM (like DNA) registered it)
# - read it now (and try to register as {imageTemplate}_kappa_settings.xml)
# - just use the datum (0,0,0)
'''
#code for using a predefined datum (0;0;0)
#EDUtilsFile.writeFile( EDDiskExplorer.mergePath( self.getWorkingDirectory(), "DNA_STAC_Kappa_Settings" ), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>0.000000</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>0</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>")
# gonio settings from DC descriptor object
EDFactoryPluginStatic.loadModule("XSDataMXv2")
#import XSDataMXv2
#dc = XSDataMXv2.XSDataCollection()
from XSDataMXv2 import XSDataCollection
dc = XSDataCollection()
dc = self.getDataInput("dataCollection")[0]
omega = dc.getXSSubWedge()[0].getXSRotationalGoniostatSetting().getBaseaxissetting()
[kappa, phi] = dc.getXSSubWedge()[0].getXSRotationalGoniostatSetting().getAxissetting()
EDUtilsFile.writeFile(os.path.join(self.getWorkingDirectory(), "DNA_STAC_Kappa_Settings"), "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?><kappa_collect_settings><motorSettings><motorName>Omega</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>Kappa</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>Phi</motorName><motorValue>%e</motorValue></motorSettings><motorSettings><motorName>X</motorName><motorValue>0.261444</motorValue></motorSettings><motorSettings><motorName>Y</motorName><motorValue>-0.085559</motorValue></motorSettings><motorSettings><motorName>Z</motorName><motorValue>0.659333</motorValue></motorSettings><comment>BCM query performed by STAC</comment></kappa_collect_settings>" % (omega.getValue(), kappa.getValue(), phi.getValue()))
'''
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 generateXSDataISPyBScreeningInput(_xsDataInputControlISPyB):
"""
"""
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_2")
from XSDataISPyBv1_2 import XSDataISPyBScreeningInput
from XSDataISPyBv1_2 import XSDataDouble
xsDataResultCharacterisation = _xsDataInputControlISPyB.getCharacterisationResult()
xsDataISPyBScreeningInput = XSDataISPyBScreeningInput()
xsDataCollection = EDHandlerXSDataISPyBv2_0.getDataCollectionFromSuggestedStrategy(xsDataResultCharacterisation)
# Data collection information
if (xsDataCollection is not None):
xsDataSubWedgeList = xsDataCollection.getSubWedge()
if (xsDataSubWedgeList is not None):
xsDataSubWedgeFirst = xsDataSubWedgeList[0]
xsDataExperimentalCondition = xsDataSubWedgeFirst.getExperimentalCondition()
if (xsDataExperimentalCondition is not None):
xsDataDetector = xsDataExperimentalCondition.getDetector()
if (xsDataDetector is not None):
fBeamPositionX = xsDataDetector.getBeamPositionX().getValue()
fBeamPositionY = xsDataDetector.getBeamPositionY().getValue()
xsDataISPyBScreeningInput.setBeamX(XSDataDouble(fBeamPositionX))
xsDataISPyBScreeningInput.setBeamY(XSDataDouble(fBeamPositionY))
return xsDataISPyBScreeningInput
def testCreateOutputFileDictionary(self):
strPathToCCP4iResult = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultCCP4i_reference.xml")
strXML = self.readAndParseFile(strPathToCCP4iResult)
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataResultCCP4i
xsDataResultCCP4i = XSDataResultCCP4i.parseString(strXML)
xsDataStringListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles(
)
pluginMXCuBE = self.createPlugin()
pluginMXCuBE.configure()
strResultCharacterisationFileName = "XSDataResultCharacterisation_reference.xml"
strPathToReferenceFile = os.path.join(
self.getPluginTestsDataHome(), strResultCharacterisationFileName)
strXML = self.readAndParseFile(strPathToReferenceFile)
xsDataResultCharacterisation = XSDataResultCharacterisation.parseString(
strXML)
strDNAFileDirectoryPath = pluginMXCuBE.createDNAFileDirectoryPath(
xsDataResultCharacterisation)
pluginMXCuBE.createDNAFileDirectory(strDNAFileDirectoryPath)
xsDataDictionary = pluginMXCuBE.createOutputFileDictionary(
xsDataStringListOfOutputFiles, xsDataResultCharacterisation,
strDNAFileDirectoryPath)
EDAssert.equal(False, xsDataDictionary is None)
shutil.rmtree(strDNAFileDirectoryPath)
def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
# Checks the expected result
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
# strObtainedOutput = plugin.getDataOutput().marshal() # EDUtilsTest.readAndParseFile ( self.m_edObtainedOutputDataFile )
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultDiffractionCT.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()# XSDataResultDiffractionCT.parseString(strObtainedOutput)
EDAssert.equal(xsDataResultReference.marshal(), xsDataResultObtained.marshal())
ref = self.readAndParseFile(os.path.join(self.getTestsDataImagesHome(), "DCT2011March.chi"))
obt = self.readAndParseFile(xsDataResultObtained.getIntegratedIntensities().getPath().getValue())
EDAssert.strAlmostEqual(ref, obt, "Chi files are the same", 0.001)
# clean up SPD when finished
EDFactoryPluginStatic.loadPlugin("EDPluginSPDCorrectv10").killAllWorkers()
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
#self.setXSDataInputClass( XSDataInputCharacterisation )
#self.setXSDataInputClass(EDList)
#self.strPluginIndexingName = "EDPluginControlIndexingv2_0"
self.strPluginIndexingName = "EDPluginControlIndexingv10"
self.edPluginIndexing = None
self.strPluginIntegrationName = "EDPluginControlIntegrationv10"
self.edPluginIntegration = None
self.xsDataResultCharacterisationv2_0 = None
self.xsDataResultCharacterisation = None
self.xsDataInputStrategy = None
self.setXSDataInputClass(XSDataInputCharacterisationv2_0)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataInputCharacterisation,
"mxv1InputCharacterisation")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
def mergeAtomicComposition(self, _xsDataAtomicComposition1,
_xsDataAtomicComposition2):
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
mergedAtomicComposition = XSDataAtomicComposition()
dictionary = {}
for atom in _xsDataAtomicComposition2.getAtom():
dictionary[
atom.getSymbol().getValue()] = atom.getNumberOf().getValue()
for atom1 in _xsDataAtomicComposition1.getAtom():
symbol = atom1.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition2) == True):
mergedAtom = XSDataAtom()
mergedAtom.setNumberOf(
XSDataDouble(atom1.getNumberOf().getValue() +
dictionary[symbol]))
mergedAtom.setSymbol(XSDataString(symbol))
mergedAtomicComposition.addAtom(mergedAtom)
else:
mergedAtomicComposition.addAtom(atom1)
for atom2 in _xsDataAtomicComposition2.getAtom():
symbol = atom2.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition1) == False):
mergedAtomicComposition.addAtom(atom2)
return mergedAtomicComposition
def preProcess(self, _edPlugin=None):
"""
This method prepares the input for the CCP4i plugin and loads it.
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.preProcess...")
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataInputCCP4i
xsDataInputCCP4i = XSDataInputCCP4i()
xsDataInputMXCuBE = self.getDataInput()
xsDataInputCCP4i.setDataSet(xsDataInputMXCuBE.getDataSet())
#xsDataInputCCP4i.setDataFile( xsDataInputMXCuBE.getDataFile() )
xsDataInputCCP4i.setExperimentalCondition(xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputCCP4i.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputCCP4i.setSample(xsDataInputMXCuBE.getSample())
self.__edPluginControlCCP4i = self.loadPlugin(self.__strPluginControlCCP4i, "CCP4i")
self.__edPluginControlCCP4i.setDataInput(xsDataInputCCP4i)
self.__xsDataIntegerDataCollectionId = xsDataInputMXCuBE.getDataCollectionId()
if (self.__xsDataIntegerDataCollectionId is not None):
self.__edPluginControlISPyB = self.loadPlugin(self.__strPluginControlISPyB, "ISPyB")
self.__edPluginExecOutputHTML = self.loadPlugin(self.__strPluginExecOutputHTMLName, "OutputHTML")
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
from XSDataMXv2 import XSDataCollection
self.setXSDataInputClass(XSDataCollection, "dataCollection")
self.__pyStrBCMDEF = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
from XSDataMXv2 import XSDataCollection
self.setXSDataInputClass(XSDataCollection, "dataCollection")
self.__pyStrBCMDEF = None
def runMXv1Pipeline():
strLogFileName = os.path.join(returnWorkingDirectory(), "wsgi-server.log")
EDVerbose.setLogFileName(strLogFileName)
strInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if strInput:
# Take the parameters string, split off the title and run the bash script to generate the input char. XML
listParams = shlex.split(strInput)
strComments = listParams[0] # the 1st item
strShortComments = listParams[1] # the 2nd item
strWorkingDir = listParams[2] # the 3rd item
strHTMLResultDir = listParams[3] # the 4th item
os.chdir(strWorkingDir)
strParamString = " ".join(listParams[4:]) # all but the first four items
edPluginMxv1ParamsToXML = EDFactoryPluginStatic.loadPlugin('EDPluginMxv1ParamsToXMLv1_0')
edPluginMxv1ParamsToXML.setDataInput(XSDataString(strParamString), "paramString")
edPluginMxv1ParamsToXML.executeSynchronous()
xsDataFile = edPluginMxv1ParamsToXML.getDataOutput()
# Read the XML and parse it into an object hierarchy
strXMLFile = xsDataFile.getPath().getValue()
f = open(strXMLFile, 'r')
xml = f.read()
f.close()
xsDataInputCharacterisation = XSDataInputCharacterisation.parseString(xml)
# Run the MXv1 application pipeline
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath, \
_xsDataInputCharacterisation=xsDataInputCharacterisation, \
_strComments=strComments, \
_strShortComments=strShortComments)
edApplicationMXv1Characterisation.execute()
# Run the EDNA2HTML generator on the output from the MXv1 application
edPluginExecOutputHTML = EDFactoryPluginStatic.loadPlugin('EDPluginExecOutputHTMLv1_0')
edPluginExecOutputHTML.setDataInput(XSDataString(strComments), "title")
strWorkingDir = os.path.join(strWorkingDir, edApplicationMXv1Characterisation.getWorkingDir())
edPluginExecOutputHTML.setDataInput(XSDataString(strWorkingDir), "workingDir")
#strBaseDir = os.path.join(strHTMLResultDir, "edna")
#edPluginExecOutputHTML.setDataInput(XSDataString(strBaseDir), "basename")
edPluginExecOutputHTML.setDataInput(XSDataString(strHTMLResultDir), "basename")
edPluginExecOutputHTML.executeSynchronous()
strPathToHTMLFile = ""
if (edPluginExecOutputHTML.hasDataOutput("htmlFile")):
strPathToHTMLFile = edPluginExecOutputHTML.getDataOutput("htmlFile")[0].getPath().getValue()
else:
EDVerbose.ERROR("edna-mxv1-wsgi-server: edPluginExecOutputHTML has no dataOutput htmlFile!")
if strPathToHTMLFile =="":
EDVerbose.ERROR("edna-mxv1-wsgi-server: Returning empty string")
return strPathToHTMLFile
else:
return strInput
def __init__(self, _strNameOfPlugin):
EDPlugin.__init__(self)
self.__strNameOfPlugin = _strNameOfPlugin
EDFactoryPluginStatic.loadModule(_strNameOfPlugin)
self.__dictXMLDataInput = {}
self.__dictXMLDataOutput = {}
self.__strPythonWrapperScriptName = "pluginWrapperForJobScheduler.py"
self.__strPathToPythonWrapper = None
self.__edServerXMLRCP = EDServerXMLRCP.getInstance()
self.__edServerXMLRCP.registerPlugin(self)
self.__bFinished = False
def __init__(self):
"""
"""
EDPluginSTACv2_0.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataMXv1 import XSDataIndexingResult
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass(XSDataInputBest, "inputBest")
self.setXSDataInputClass(XSDataIndexingResult, "indexingResult")
from XSDataMXv1 import XSDataString
self.setXSDataInputClass(XSDataString, "KappaStrategyOption")
def __init__(self):
"""
"""
EDPluginSTACv2_0.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataMXv1 import XSDataIndexingResult
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass(XSDataInputBest, "inputBest")
self.setXSDataInputClass(XSDataIndexingResult, "indexingResult")
from XSDataMXv1 import XSDataString
self.setXSDataInputClass(XSDataString, "KappaStrategyOption")
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataInputISPyB = EDHandlerXSDataISPyBv1_4.generateXSDataInputISPyBStoreScreening(xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = EDUtilsFile.readFileAndParseVariables(strReferencePath, self.dictReplace)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_4")
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataInputISPyB = EDHandlerXSDataISPyBv1_3.generateXSDataInputISPyBStoreScreening(xsDataInputControlISPyB)
print xsDataInputISPyB.marshal()
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = EDUtilsFile.readFileAndParseVariables(strReferencePath, self.dictReplace)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_3")
def testGetXSDataResultCharacterisation(self):
strPathToCCP4iResult = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultCCP4i_reference.xml")
strXML = self.readAndParseFile(strPathToCCP4iResult)
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataResultCCP4i
xsDataResultCCP4i = XSDataResultCCP4i.parseString(strXML)
strListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles().getValue()
pluginMXCuBE = self.createPlugin()
xsDataResultCharacterisation = pluginMXCuBE.getXSDataResultCharacterisation(strListOfOutputFiles)
strPathToResultCharacterisationReference = os.path.join(self.getPluginTestsDataHome(),
"EDPluginControlCharacterisationv1_1_dataOutput.xml")
xsDataResultCharacterisationReference = XSDataResultCharacterisation.parseFile(strPathToResultCharacterisationReference)
EDAssert.equal(xsDataResultCharacterisationReference.marshal(), xsDataResultCharacterisation.marshal())
def testGenerateXSDataMOSFLMInputIntegration(self):
strFilename = "XSDataIntegrationInput_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLIntegrationInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInput = XSDataIntegrationInput.parseString(strXMLIntegrationInput)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(xsDataIntegrationInput)
strReferenceFilename = "XSDataMOSFLMInputIntegration_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath, strReferenceFilename)
strXMLIntegrationInputReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
xsDataMOSFLMInputIntegrationReference = XSDataMOSFLMInputIntegration.parseString(strXMLIntegrationInputReference)
EDAssert.equal(xsDataMOSFLMInputIntegrationReference.marshal(), xsDataMOSFLMInputIntegration.marshal())
def getPathToProjectConfigurationFile(self, _strPluginName):
"""
This method returns the path to the Project configuration file.
@param _strPluginName: Name of the module
@type _strPluginName: python string
@return: The path to the project configuration file
@type: python string
"""
strPathToProjectConfigurationFile = None
strCurrentDirectory = EDFactoryPluginStatic.getModuleLocation(_strPluginName)
if strCurrentDirectory is None:
self.WARNING("Cannot find path to configuration for plugin %s" % _strPluginName)
else:
with self.locked():
bConfFileFound = False
strPathToProjectConfigurationFile = None
strConfigurationFileBaseName = "XSConfiguration_%s" % EDUtilsPath.EDNA_SITE
while not bConfFileFound:
strPreviousDirectory = strCurrentDirectory
strCurrentDirectory = os.path.dirname(strCurrentDirectory)
if strCurrentDirectory in (EDUtilsPath.EDNA_HOME, strPreviousDirectory):
strPathToProjectConfigurationFile = None
break
strPathToConfigurationDirectory = os.path.abspath(os.path.join(strCurrentDirectory, "conf"))
for ext in [".json", ".xml"]:
strPathToProjectConfigurationFile = os.path.abspath(os.path.join(strPathToConfigurationDirectory, \
strConfigurationFileBaseName + ext))
self.DEBUG("Looking for configuration file for %s in %s" %
(_strPluginName, strPathToProjectConfigurationFile))
bConfFileFound = os.path.isfile(strPathToProjectConfigurationFile)
if bConfFileFound:
break
return strPathToProjectConfigurationFile
def getConfigurationHome(_strPluginName):
"""
Returns the configuration directory path for a given test module
"""
strModuleLocation = EDFactoryPluginStatic.getFactoryPlugin().getModuleLocation(_strPluginName)
strConfigurationHome = EDUtilsPath.appendListOfPaths(strModuleLocation, [ "..", "..", "..", "conf" ])
return strConfigurationHome
def preProcess(self):
"""
Initialize the plugin to be launched
"""
EDTestCasePlugin.preProcess(self)
if(EDUtilsPath.EDNA_SITE == None):
raise RuntimeError, "EDNA_SITE must be set"
# Load the plugin that should be executed
self._edPlugin = EDFactoryPluginStatic.loadPlugin(self.getPluginName())
if(self._edPlugin is not None):
for strInputDataKey in self._dictStrDataInputFiles.keys():
if (type(self._dictStrDataInputFiles[ strInputDataKey ]) == types.ListType):
for strDataInputFile in self._dictStrDataInputFiles[ strInputDataKey ]:
strXMLData = self.readAndParseFile(strDataInputFile)
if (strInputDataKey == self._strDefaultInputDataKey):
self._edPlugin.setDataInput(strXMLData)
else:
self._edPlugin.setDataInput(strXMLData, strInputDataKey)
else:
strXMLData = self.readAndParseFile(self._dictStrDataInputFiles[ strInputDataKey ])
if (strInputDataKey == self._strDefaultInputDataKey):
self._edPlugin.setDataInput(strXMLData)
else:
self._edPlugin.setDataInput(strXMLData, strInputDataKey)
#self._edPlugin.setDataInput( self._strXMLData, "inputMXCuBE" )
else:
EDVerbose.ERROR("Cannot load plugin: %s" % self.getPluginName())
raise RuntimeError
self._edPlugin.setConfiguration(self.getPluginConfiguration())
def testGenerateXSDataIndexingResult(self):
"""
This method tests the generation of an XSDataIndexingResult object given an XSDataResultLabelit object.
"""
strPath = os.path.join(self.strDataPath, self.strReferenceOutputFile)
strXMLResultLabelit = EDUtilsTest.readAndParseFile(strPath)
EDFactoryPluginStatic.loadModule("XSDataLabelitv10")
from XSDataLabelitv10 import XSDataResultLabelit
xsDataResultLabelit = XSDataResultLabelit.parseString(strXMLResultLabelit)
from EDHandlerXSDataLabelitv10 import EDHandlerXSDataLabelitv10
xsDataIndexingResult = EDHandlerXSDataLabelitv10.generateXSDataIndexingResult(xsDataResultLabelit)
strReferencePath = os.path.join(self.strDataPath, "XSDataIndexingResult_reference.xml")
strIndexingResultReferenceXML = EDUtilsTest.readAndParseFile(strReferencePath)
from XSDataMXv1 import XSDataIndexingResult
xsDataIndexingResultReference = XSDataIndexingResult.parseString(strIndexingResultReferenceXML)
EDAssert.equal(xsDataIndexingResultReference.marshal(), xsDataIndexingResult.marshal())
def process(self):
"""
Calls the Plugin to be executed
"""
EDVerbose.DEBUG("EDApplicationDimplev0.process")
if (not self.isFailure()):
edPlugin = EDFactoryPluginStatic.loadPlugin(self.getPluginName())
if (edPlugin is not None):
edPlugin.setBaseDirectory(
self.getFullApplicationWorkingDirectory())
edPlugin.setBaseName(self.getPluginName())
if self.ccp4DataInputControlPipelineCalcDiffMap is None:
self.ccp4DataInputControlPipelineCalcDiffMap = self.createInput(
)
edPlugin.setDataInput(
self.ccp4DataInputControlPipelineCalcDiffMap)
edPlugin.connectSUCCESS(self.doSuccessActionPlugin)
edPlugin.connectFAILURE(self.doFailureActionPlugin)
EDVerbose.DEBUG("EDApplicationDimplev0.process: Executing " +
self.getPluginName())
edPlugin.execute()
edPlugin.synchronize()
else:
EDVerbose.error(
"EDApplicationDimplev0.process : plugin not loaded : %s" %
self.getPluginName())
self.setFailure(True)
def process(self):
"""
Calls the Plugin to be executed
"""
EDVerbose.DEBUG("EDApplicationXAFSDataProcessing.process")
if (not self.isFailure()) and (self.__bProcess):
edPlugin = EDFactoryPluginStatic.loadPlugin(self.getPluginName())
if (edPlugin is not None):
edPlugin.setBaseDirectory(
self.getFullApplicationWorkingDirectory())
edPlugin.setBaseName(self.getPluginName())
self.setPluginInput(edPlugin)
edPlugin.connectSUCCESS(self.doSuccessActionPlugin)
edPlugin.connectFAILURE(self.doFailureActionPlugin)
EDVerbose.DEBUG(
"EDApplicationXAFSDataProcessing.process: Executing " +
self.getPluginName())
edPlugin.execute()
edPlugin.synchronize()
else:
EDVerbose.error(
"EDApplicationXAFSDataProcessing .process : plugin not loaded : %s"
% self.getPluginName())
self.setFailure(True)
def loadCalibratedData(self, _strElementName):
"""
This method reads a file containing the calibrated energy spectra
"""
calibratedData = None
strModuleLocation = EDFactoryPluginStatic.getModuleLocation(
self.getPluginName())
strEnergyDataFile = os.path.join(os.path.dirname(strModuleLocation),
"calibrationData",
_strElementName + ".dat")
if os.path.exists(strEnergyDataFile):
listLines = []
with open(strEnergyDataFile, 'r') as f:
listLines = f.readlines()
iSkipHeader = 0
iSkipFooter = 0
bIsHeader = True
for strLine in listLines:
if strLine.startswith('#'):
if bIsHeader:
iSkipHeader += 1
else:
iSkipFooter += 1
else:
bIsHeader = False
calibratedData = numpy.genfromtxt(strEnergyDataFile,
skip_header=iSkipHeader,
skip_footer=iSkipFooter)
return calibratedData
def testGenerateXSDataInputLabelit(self, _strFileNameXSDataIndexingInput_reference,
_strFileNameXSDataLabelitInput_reference):
"""
This method is testing the generation of the XSDataInputLabelit object given a XSDataIndexingInput object.
"""
strPath = os.path.join(self.strDataPath, _strFileNameXSDataIndexingInput_reference)
strXMLIndexingInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIndexingInput
xsDataIndexingInput = XSDataIndexingInput.parseString(strXMLIndexingInput)
from EDHandlerXSDataLabelitv10 import EDHandlerXSDataLabelitv10
xsDataInputLabelit = EDHandlerXSDataLabelitv10.generateXSDataInputLabelit(xsDataIndexingInput)
strReferencePath = os.path.join(self.strDataPath, _strFileNameXSDataLabelitInput_reference)
strXMLInputLabelitReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataLabelitv10")
from XSDataLabelitv10 import XSDataInputLabelit
xsDataInputLabelitReference = XSDataInputLabelit.parseString(strXMLInputLabelitReference)
EDAssert.equal(xsDataInputLabelitReference.marshal(), xsDataInputLabelit.marshal())
def __init__(self):
EDPluginControl.__init__(self)
#self.setXSDataInputClass(EDList)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult,
"mxv1IndexingResult")
#disable kappa by default
self.KappaStrategy = 0
self.strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.strSymopHome = os.path.normpath("/opt/pxsoft/ccp4-6.0.2/lib/data")
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
def testGenerateXSDataInputBestv1_2(self, _strFileNameXSDataInputStrategy_reference, _strFileNameXSDataInputBest_reference):
"""
This method is testing the generation of the XSDataInputBest object given a XSDataIndexingStrategy object.
"""
strReferenceInputFile = os.path.join(self.strDataPath, _strFileNameXSDataInputStrategy_reference)
strPath = os.path.join(self.strDataPath, strReferenceInputFile)
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategy = XSDataInputStrategy.parseFile(strPath)
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
edHandlerXSDataBestv1_2 = EDHandlerXSDataBestv1_2()
xsDataInputBestv1_2 = edHandlerXSDataBestv1_2.getXSDataInputBest(xsDataInputStrategy)
strReferencePath = os.path.join(self.strDataPath, _strFileNameXSDataInputBest_reference)
strXMLInputBestReference = EDUtilsTest.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBestReference = XSDataInputBest.parseString(strXMLInputBestReference)
EDAssert.equal(xsDataInputBestReference.marshal(), xsDataInputBestv1_2.marshal())
def __init__(self):
EDPluginControl.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection, "mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult, "mxv1IndexingResult")
# disable kappa by default
self.KappaStrategy = 0
self.strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.strSymopHome = os.path.normpath("/opt/pxsoft/ccp4-6.0.2/lib/data")
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
def configure(self):
EDPluginExec.configure(self)
EDVerbose.DEBUG("EDPluginExecOutputHTMLv1_0.configure")
self.strEDNA2html = self.config.get(self.CONF_EDNA2html)
if self.strEDNA2html is None and os.environ.has_key("EDNA2html"):
self.strEDNA2html = os.environ["EDNA2html"]
else:
self.strEDNA2html = EDFactoryPluginStatic.getModuleLocation("EDNA2html")
pass
def generateXSDataInputLabelitIndexing(_xsDataIndexingInput):
EDFactoryPluginStatic.loadModule("XSDataPhenixv1_1")
from XSDataPhenixv1_1 import XSDataInputLabelitIndexing
inputLabelitIndexing = XSDataInputLabelitIndexing()
listXSDataImageReference = []
dataCollection = _xsDataIndexingInput.dataCollection
for subWedge in dataCollection.subWedge:
for image in subWedge.image:
inputLabelitIndexing.image.append(image.copy())
xsDataCrystal = _xsDataIndexingInput.getCrystal()
if xsDataCrystal is not None:
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if xsDataSpaceGroup is not None:
xsDataStringName = xsDataSpaceGroup.getName()
if xsDataStringName is not None:
inputLabelitIndexing.forcedSpaceGroup = xsDataStringName
return inputLabelitIndexing
def generateXSDataInputLabelitIndexing(_xsDataIndexingInput):
EDFactoryPluginStatic.loadModule("XSDataPhenixv1_1")
from XSDataPhenixv1_1 import XSDataInputLabelitIndexing
inputLabelitIndexing = XSDataInputLabelitIndexing()
listXSDataImageReference = []
dataCollection = _xsDataIndexingInput.dataCollection
for subWedge in dataCollection.subWedge:
for image in subWedge.image:
inputLabelitIndexing.image.append(image.copy())
xsDataCrystal = _xsDataIndexingInput.getCrystal()
if xsDataCrystal is not None:
xsDataSpaceGroup = xsDataCrystal.getSpaceGroup()
if xsDataSpaceGroup is not None:
xsDataStringName = xsDataSpaceGroup.getName()
if xsDataStringName is not None:
inputLabelitIndexing.forcedSpaceGroup = xsDataStringName
return inputLabelitIndexing
def mergeStrategyToNewOrientation(_xsDataResultStrategy, _xsDataCollection, _fOmega, _fKappa, _fPhi):
'''
_xsDataResultStrategy: reference strategy results as the template for the new strategy
_xsDataCollection: The data collection that will be merged in
result:
suggestedStrategy(XSDataResultStrategy): the strategy resulted from the merge
'''
# suggestedStrategy = None
# try:
# newpossibleOrientations=XSDataSTACv01.kappa_alignment_response.parseString(_possible_orientation.marshal())
# except:
# newpossibleOrientations=None
#so we will copy the strategy of collecting the reference images inputed to here but at the new orientation
#get the full strategy from the Reference
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
suggestedStrategy = XSDataResultStrategy.parseString(_xsDataResultStrategy.marshal())
#take only the first CollectionPlan
if len(suggestedStrategy.getCollectionPlan()) > 0:
suggestedStrategy.setCollectionPlan([suggestedStrategy.getCollectionPlan()[0]])
#modify the DC part taking it from the input
suggestedStrategy.getCollectionPlan()[0].setCollectionStrategy(_xsDataCollection)
#and modify the Orientation
# dc = XSDataMXv2.XSDataCollection()
# dc = self.getDataInput("mxv2DataCollection_Reference")[0]
# Orients = _possible_orientation.getPossible_orientation()
# omega = Orients[0].getOmega()
# kappa = Orients[0].getKappa()
# phi = Orients[0].getPhi()
suggestedStrategy = EDHandlerXSDataMXv1v1_0.copyStrategyToNewOrientation(suggestedStrategy, _fOmega, _fKappa, _fPhi, "MERGED")
# for dcplan in suggestedStrategy.getCollectionPlan():
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "OMEGA=", omega))
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "KAPPA=", kappa))
# dcplan.setComment(EDHandlerXSDataMXv1v1_0().replaceElements(dcplan.getComment(), "PHI=", phi))
#finally take the suggested new orientation out of the list of further possible ones
# if newpossibleOrientations is not None:
# newpossibleOrientations.setPossible_orientation([])
# for i in range(1, Orients.__len__()):
# if (math.fabs(float(Orients[i].getKappa())-float(kappa))<tol and math.fabs(float(Orients[i].getPhi())-float(phi))<tol):
# newpossibleOrientations.addPossible_orientation(Orients[i])
# return [suggestedStrategy,newpossibleOrientations]
return suggestedStrategy
def configure(self):
EDPluginExec.configure(self)
EDVerbose.DEBUG("EDPluginExecOutputHTMLv1_0.configure")
self.strEDNA2html = self.config.get(self.CONF_EDNA2html)
if self.strEDNA2html is None and os.environ.has_key("EDNA2html"):
self.strEDNA2html = os.environ["EDNA2html"]
else:
self.strEDNA2html = EDFactoryPluginStatic.getModuleLocation(
"EDNA2html")
pass
def testGetXSDataResultCharacterisation(self):
strPathToCCP4iResult = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultCCP4i_reference.xml")
strXML = self.readAndParseFile(strPathToCCP4iResult)
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataResultCCP4i
xsDataResultCCP4i = XSDataResultCCP4i.parseString(strXML)
strListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles(
).getValue()
pluginMXCuBE = self.createPlugin()
xsDataResultCharacterisation = pluginMXCuBE.getXSDataResultCharacterisation(
strListOfOutputFiles)
strPathToResultCharacterisationReference = os.path.join(
self.getPluginTestsDataHome(),
"EDPluginControlCharacterisationv1_1_dataOutput.xml")
xsDataResultCharacterisationReference = XSDataResultCharacterisation.parseFile(
strPathToResultCharacterisationReference)
EDAssert.equal(xsDataResultCharacterisationReference.marshal(),
xsDataResultCharacterisation.marshal())
def getXSDataMOSFLMDetector(_xsDataDetector):
"""
Translates an XSDataDetector object to XSDataMOSFLMv10.
"""
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMDetector
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
strDetectorType = _xsDataDetector.getType().getValue()
if (strDetectorType == "q4") or \
(strDetectorType == "q4-2x") or \
(strDetectorType == "q210") or \
(strDetectorType == "q210-2x") or \
(strDetectorType == "q315") or \
(strDetectorType == "q315-2x"):
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
elif (strDetectorType == "mar165") or \
(strDetectorType == "mar225"):
xsDataMOSFLMDetector.setType(XSDataString("MARCCD"))
elif (strDetectorType == "pilatus6m"
or strDetectorType == "pilatus2m"):
xsDataMOSFLMDetector.setType(XSDataString("PILATUS"))
elif strDetectorType.startswith("eiger2"):
xsDataMOSFLMDetector.setType(XSDataString("EIGER2"))
elif strDetectorType.startswith("eiger"):
xsDataMOSFLMDetector.setType(XSDataString("EIGER"))
elif (strDetectorType == "raxis4"):
xsDataMOSFLMDetector.setType(XSDataString("RAXISIV"))
else:
# This is a temporary solution for the exception problem pointed out in bug #43.
# Instead of raising an exception with a known type we send the error message as a string.
strErrorMessage = "EDHandlerXSDataMOSFLMv10.getXSDataMOSFLMDetector: Unknown detector type : " + strDetectorType
raise BaseException(strErrorMessage)
if (_xsDataDetector.getNumberPixelX() is not None):
xsDataMOSFLMDetector.setNumberPixelX(
_xsDataDetector.getNumberPixelX())
if (_xsDataDetector.getNumberPixelY() is not None):
xsDataMOSFLMDetector.setNumberPixelY(
_xsDataDetector.getNumberPixelY())
if (_xsDataDetector.getPixelSizeX() is not None):
xsDataMOSFLMDetector.setPixelSizeX(_xsDataDetector.getPixelSizeX())
if (_xsDataDetector.getPixelSizeY() is not None):
xsDataMOSFLMDetector.setPixelSizeY(_xsDataDetector.getPixelSizeY())
return xsDataMOSFLMDetector
def runXAFSPipeline():
xmlXSDataInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if xmlXSDataInput:
edPluginControlXAFSDataProcessing = EDFactoryPluginStatic.loadPlugin('EDPluginControlXAFSDataBatchProcessingv0_1')
edPluginControlXAFSDataProcessing.setDataInput(xmlXSDataInput)
edPluginControlXAFSDataProcessing.executeSynchronous()
return os.path.join(edPluginControlXAFSDataProcessing.getWorkingDirectory(), \
edPluginControlXAFSDataProcessing.returnResultsFilename())
else:
return xmlXSDataInput
def preProcess(self):
"""
PreProcess of the execution test: download an EDF file from http://www.edna-site.org
"""
EDTestCasePluginExecuteControlMedianFilterImagev1_0.preProcess(self)
self.loadTestImage([ "noise2.edf", "noise3.edf", "noise4.edf", "noise5.edf", "noise6.edf"])
acc = EDFactoryPluginStatic.loadPlugin("EDPluginAccumulatorv1_0")
xsdIn = XSDataInputAccumulator()
xsdIn.setItem([XSDataString(os.path.join(self.getTestsDataImagesHome(), "noise%i.edf" % i)) for i in [2, 3, 5, 6]])
acc.setDataInput(xsdIn)
acc.executeSynchronous()
def testCreateOutputFileDictionary(self):
strPathToCCP4iResult = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultCCP4i_reference.xml")
strXML = self.readAndParseFile(strPathToCCP4iResult)
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataResultCCP4i
xsDataResultCCP4i = XSDataResultCCP4i.parseString(strXML)
xsDataStringListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles()
pluginMXCuBE = self.createPlugin()
pluginMXCuBE.configure()
strResultCharacterisationFileName = "XSDataResultCharacterisation_reference.xml"
strPathToReferenceFile = os.path.join(self.getPluginTestsDataHome(),
strResultCharacterisationFileName)
strXML = self.readAndParseFile(strPathToReferenceFile)
xsDataResultCharacterisation = XSDataResultCharacterisation.parseString(strXML)
strDNAFileDirectoryPath = pluginMXCuBE.createDNAFileDirectoryPath(xsDataResultCharacterisation)
pluginMXCuBE.createDNAFileDirectory(strDNAFileDirectoryPath)
xsDataDictionary = pluginMXCuBE.createOutputFileDictionary(xsDataResultCharacterisation, strDNAFileDirectoryPath)
EDAssert.equal(False, xsDataDictionary is None)
shutil.rmtree(strDNAFileDirectoryPath)
def preProcess(self):
"""
Creates the application working directory (log dir)
Initializes the configuration
retrieves the plugin xml data to be passed to the plugin
"""
EDVerbose.DEBUG("EDApplication.preProcess")
self.processCommandline()
if (not self.__bIsFailure):
# Check that the plugin can be located
strPluginLocation = EDFactoryPluginStatic.getFactoryPlugin().getModuleLocation(self.__strPluginName)
if (strPluginLocation is None):
EDVerbose.error("Plugin %s cannot be loaded!" % self.__strPluginName)
self.__bIsFailure = True
# Check that the input file can be read
if (self.getDataInputFilePath() is not None) and (not os.path.exists(self.__strDataInputFilePath)):
EDVerbose.error("Input XML file not found : %s" % self.__strDataInputFilePath)
self.__bIsFailure = True
# Check that the output file can be created
if (self.__strDataOutputFilePath is not None):
strOutputDirectory = os.path.dirname(self.__strDataOutputFilePath)
if (strOutputDirectory is None or strOutputDirectory == ""):
strOutputDirectory = os.getcwd()
self.__strDataOutputFilePath = os.path.join(strOutputDirectory, self.__strDataOutputFilePath)
if (not os.access(strOutputDirectory, os.W_OK)):
EDVerbose.error("Output directory not writable: %s" % strOutputDirectory)
self.__bIsFailure = True
elif (os.path.exists(self.__strDataOutputFilePath)):
if (not os.access(self.__strDataOutputFilePath, os.W_OK)):
EDVerbose.error("Output file not writable: %s" % self.__strDataOutputFilePath)
self.__bIsFailure = True
if (not self.__bIsFailure):
EDVerbose.DEBUG("EDApplication.PLUGIN_PARAM_LABEL: " + EDApplication.PLUGIN_PARAM_LABEL)
# Load the configuration file
if(self.__strConfigurationFileName is None):
self.__strConfigurationHome = EDApplication.getConfigurationHome(self.__strPluginName)
self.__strConfigurationFileName = os.path.abspath(os.path.join(self.__strConfigurationHome, "XSConfiguration_%s.xml" % EDUtilsPath.getEdnaSite()))
if (os.path.exists(self.__strConfigurationFileName)):
EDVerbose.screen("Loading Configuration file: %s" % self.__strConfigurationFileName)
edConfiguration = EDConfiguration(self.__strConfigurationFileName)
self.setConfiguration(edConfiguration)
self.loadConfiguration()
EDVerbose.DEBUG("EDApplication.preProcess: Checking... Number of plugins...: %d" % EDApplication.__edConfiguration.getPluginListSize())
pyDictionary = {}
pyDictionary[ "${EDNA_HOME}" ] = EDUtilsPath.getEdnaHome()
if self.getDataInputFilePath() is not None:
self.__strXMLData = EDUtilsFile.readFileAndParseVariables(self.getDataInputFilePath(), pyDictionary)
else:
EDVerbose.warning("Cannot find configuration file: %s" % self.__strConfigurationFileName)
# Create the application working directory
if(self.__strWorkingDir is None):
self.__strWorkingDir = self.__strApplicationInstanceName
self.createApplicationWorkingDirectory()
def __init__(self):
EDPluginControl.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult,
"mxv1IndexingResult")
# disable kappa by default
self.KappaStrategy = 0
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = self.readAndParseFile(strPath)
from XSDataMXv1 import XSDataInputControlISPyB
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
from EDHandlerXSDataISPyBv1_1 import EDHandlerXSDataISPyBv1_1
xsDataInputISPyB = EDHandlerXSDataISPyBv1_1.generateXSDataInputISPyB(xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = self.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataInputISPyB
xsDataInputISPyBReference = XSDataInputISPyB.parseString(strXMLInputISPyBReference)
# Remove the time strings since they otherwise make the test fail
xsDataInputISPyBReference.getScreening().setTimeStamp(None)
xsDataInputISPyB.getScreening().setTimeStamp(None)
EDAssert.equal(xsDataInputISPyBReference.marshal(), xsDataInputISPyB.marshal())
def copyStrategyToNewOrientation(_xsDataResultStrategy, _fOmega, _fKappa, _fPhi, _strategy = "COPIED"):
'''
_xsDataResultStrategy: the strategy results in which the orientation should be changed
omega,kappa,phi: the new orientation
result:
suggestedStrategy(XSDataResultStrategy): the strategy in which the orientation is changed
'''
#we suggest the currently calculated strategy
EDFactoryPluginStatic.loadModule("XSDataMXv1")
from XSDataMXv1 import XSDataResultStrategy
suggestedStrategy = XSDataResultStrategy.parseString(_xsDataResultStrategy.marshal())
#and we have to add the actual orientation
EDFactoryPluginStatic.loadModule("EDHandlerXSDataCommon")
from EDHandlerXSDataCommon import EDHandlerXSDataCommon
for dcplan in suggestedStrategy.getCollectionPlan():
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "OMEGA=", str(_fOmega)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "KAPPA=", str(_fKappa)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "PHI=", str(_fPhi)))
dcplan.setComment(EDHandlerXSDataCommon.replaceElements(dcplan.getComment(), "STRATEGY=", str(_strategy)))
return suggestedStrategy
def testGenerateXSDataMOSFLMInputIntegration(self):
strFilename = "XSDataIntegrationInput_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLIntegrationInput = EDUtilsTest.readAndParseFile(strPath)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInput = XSDataIntegrationInput.parseString(
strXMLIntegrationInput)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataMOSFLMInputIntegration = EDHandlerXSDataMOSFLMv10.generateXSDataMOSFLMInputIntegration(
xsDataIntegrationInput)
strReferenceFilename = "XSDataMOSFLMInputIntegration_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath,
strReferenceFilename)
strXMLIntegrationInputReference = EDUtilsTest.readAndParseFile(
strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataMOSFLMv10")
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
xsDataMOSFLMInputIntegrationReference = XSDataMOSFLMInputIntegration.parseString(
strXMLIntegrationInputReference)
EDAssert.equal(xsDataMOSFLMInputIntegrationReference.marshal(),
xsDataMOSFLMInputIntegration.marshal())
def runXAFSPipeline():
xmlXSDataInput = str(request['wsgi.input'].read(
int(request['CONTENT_LENGTH'])))
if xmlXSDataInput:
edPluginControlXAFSDataProcessing = EDFactoryPluginStatic.loadPlugin(
'EDPluginControlXAFSDataBatchProcessingv0_1')
edPluginControlXAFSDataProcessing.setDataInput(xmlXSDataInput)
edPluginControlXAFSDataProcessing.executeSynchronous()
return os.path.join(edPluginControlXAFSDataProcessing.getWorkingDirectory(), \
edPluginControlXAFSDataProcessing.returnResultsFilename())
else:
return xmlXSDataInput
def __init__( self ):
"""
"""
EDPluginSTACv2_0.__init__( self )
EDFactoryPluginStatic.loadModule( "XSDataMXv1" )
EDFactoryPluginStatic.loadModule( "XSDataMXv2" )
EDFactoryPluginStatic.loadModule( "XSDataSTACv2_0" )
EDFactoryPluginStatic.loadModule( "XSDataBestv1_2" )
from XSDataMXv1 import XSDataIndexingResult
from XSDataMXv1 import XSDataInputStrategy
from XSDataBestv1_2 import XSDataInputBest
self.setXSDataInputClass( kappa_strategy_request, "kappa_strategy_request" )
import XSDataMXv2
self.setXSDataInputClass( XSDataMXv2.XSDataCollection, "mxv2DataCollection" )
# not used: self.setXSDataInputClass( XSDataIndexingResult, "indexingResult" )
self.setXSDataInputClass( XSDataInputStrategy, "inputBest" )