def testParseLabelitScreenOutput(self):
"""
This method test the parsing of the Labelit results in the log file.
"""
edPluginLabelitv10 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(), "labelit_v1000rc11.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataLabelitScreenOutput = edPluginLabelitv10.parseLabelitScreenOutput(strLabelitLogText)
strLabelitScreenOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataLabelitScreenOutput_reference.xml")
strLabelitScreenOutputXML = self.readAndParseFile(strLabelitScreenOutputFile)
from XSDataLabelitv10 import XSDataLabelitScreenOutput
xsDataLabelitScreenOutputReference = XSDataLabelitScreenOutput.parseString(strLabelitScreenOutputXML)
EDAssert.equal(xsDataLabelitScreenOutputReference.marshal(), xsDataLabelitScreenOutput.marshal())
def testParseLabelitScreenOutput(self):
"""
This method test the parsing of the Labelit results in the log file.
"""
edPluginLabelitv10 = self.createPlugin()
strPathToLabelitLogText = os.path.join(self.getPluginTestsDataHome(),
"labelit_v1000rc11.log")
strLabelitLogText = self.readAndParseFile(strPathToLabelitLogText)
xsDataLabelitScreenOutput = edPluginLabelitv10.parseLabelitScreenOutput(
strLabelitLogText)
strLabelitScreenOutputFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataLabelitScreenOutput_reference.xml")
strLabelitScreenOutputXML = self.readAndParseFile(
strLabelitScreenOutputFile)
from XSDataLabelitv10 import XSDataLabelitScreenOutput
xsDataLabelitScreenOutputReference = XSDataLabelitScreenOutput.parseString(
strLabelitScreenOutputXML)
EDAssert.equal(xsDataLabelitScreenOutputReference.marshal(),
xsDataLabelitScreenOutput.marshal())
def parseLabelitScreenOutput(self, _strLabelitLogText):
"""
This method parses the labelit.screen log and populates the relevant
parts of the XSDataLabelitScreenOutput object which is then returned.
"""
self.DEBUG("EDPluginLabelitv10.parseLabelitLogText")
xsDataLabelitScreenOutput = None
iIndex = 0
listLogLines = _strLabelitLogText.split("\n")
bFoundLabelitIndexingResults = False
bContinue = True
while bContinue:
if listLogLines[iIndex].find("LABELIT Indexing results:") != -1:
bFoundLabelitIndexingResults = True
bContinue = False
else:
if iIndex < (len(listLogLines) - 2):
iIndex += 1
else:
bContinue = False
if bFoundLabelitIndexingResults == False:
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginLabelitv10.parseLabelitLogText",
self.getClassName(),
"Labelit log message: %s" % _strLabelitLogText,
)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
else:
# We found some indexing results!
xsDataLabelitScreenOutput = XSDataLabelitScreenOutput()
iIndex += 1
strBeamDistanceMosaicity = listLogLines[iIndex]
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(",", "")
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace("mm", " ")
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace("=", " ")
listStringBeamDistanceMosaicity = strBeamDistanceMosaicity.split()
fBeamX = float(listStringBeamDistanceMosaicity[3])
fBeamY = float(listStringBeamDistanceMosaicity[5])
xsDataLabelitScreenOutput.setBeamCentreX(XSDataLength(fBeamX))
xsDataLabelitScreenOutput.setBeamCentreY(XSDataLength(fBeamY))
fDistance = float(listStringBeamDistanceMosaicity[7])
xsDataLabelitScreenOutput.setDistance(XSDataLength(fDistance))
fMosaicity = float(listStringBeamDistanceMosaicity[11])
xsDataLabelitScreenOutput.setMosaicity(XSDataAngle(fMosaicity))
iIndex += 3
bContinue = True
bFoundSelectedSolution = False
while bContinue:
xsDataLabelitScreenSolution = XSDataLabelitScreenSolution()
strLabelitSolution = listLogLines[iIndex]
listStringLabelitSolution = strLabelitSolution.split()
if listStringLabelitSolution[0] == ":)":
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(True))
else:
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(False))
iSolutionNumber = int(listStringLabelitSolution[1])
xsDataLabelitScreenSolution.setSolutionNumber(XSDataInteger(iSolutionNumber))
fMetricFitValue = float(listStringLabelitSolution[2])
xsDataLabelitScreenSolution.setMetricFitValue(XSDataDouble(fMetricFitValue))
strMetricFitCode = listStringLabelitSolution[3]
xsDataLabelitScreenSolution.setMetricFitCode(XSDataString(strMetricFitCode))
fRMSD = float(listStringLabelitSolution[4])
xsDataLabelitScreenSolution.setRmsd(XSDataLength(fRMSD))
iNumberOfSpots = int(listStringLabelitSolution[5])
xsDataLabelitScreenSolution.setNumberOfSpots(XSDataInteger(iNumberOfSpots))
xsDataLabelitScreenSolution.setCrystalSystem(XSDataString(listStringLabelitSolution[6]))
xsDataLabelitScreenSolution.setBravaisLattice(XSDataString(listStringLabelitSolution[7]))
xsDataCell = XSDataCell()
xsDataCell.setLength_a(XSDataLength(float(listStringLabelitSolution[8])))
xsDataCell.setLength_b(XSDataLength(float(listStringLabelitSolution[9])))
xsDataCell.setLength_c(XSDataLength(float(listStringLabelitSolution[10])))
xsDataCell.setAngle_alpha(XSDataAngle(float(listStringLabelitSolution[11])))
xsDataCell.setAngle_beta(XSDataAngle(float(listStringLabelitSolution[12])))
xsDataCell.setAngle_gamma(XSDataAngle(float(listStringLabelitSolution[13])))
xsDataLabelitScreenSolution.setUnitCell(xsDataCell)
iVolume = int(listStringLabelitSolution[14])
xsDataLabelitScreenSolution.setVolume(XSDataInteger(iVolume))
# Find the selected solution
if bFoundSelectedSolution == False:
if xsDataLabelitScreenSolution.getHappy().getValue() == True:
xsDataLabelitScreenOutput.setSelectedSolutionNumber(XSDataInteger(iSolutionNumber))
bFoundSelectedSolution = True
xsDataLabelitScreenOutput.addLabelitScreenSolution(xsDataLabelitScreenSolution)
if iIndex < (len(listLogLines) - 2):
iIndex += 1
else:
bContinue = False
return xsDataLabelitScreenOutput
def parseLabelitScreenOutput(self, _strLabelitLogText):
"""
This method parses the labelit.screen log and populates the relevant
parts of the XSDataLabelitScreenOutput object which is then returned.
"""
self.DEBUG("EDPluginLabelitv10.parseLabelitLogText")
xsDataLabelitScreenOutput = None
iIndex = 0
listLogLines = _strLabelitLogText.split('\n')
bFoundLabelitIndexingResults = False
bContinue = True
while (bContinue) :
if (listLogLines[ iIndex ].find("LABELIT Indexing results:") != -1) :
bFoundLabelitIndexingResults = True
bContinue = False
else:
if (iIndex < (len(listLogLines) - 2)):
iIndex += 1
else:
bContinue = False
if (bFoundLabelitIndexingResults == False):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginLabelitv10.parseLabelitLogText", self.getClassName(), "Labelit log message: %s" % _strLabelitLogText)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
else:
# We found some indexing results!
xsDataLabelitScreenOutput = XSDataLabelitScreenOutput()
iIndex += 1
strBeamDistanceMosaicity = listLogLines[ iIndex ]
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace(',', '')
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace('mm', ' ')
strBeamDistanceMosaicity = strBeamDistanceMosaicity.replace('=', ' ')
listStringBeamDistanceMosaicity = strBeamDistanceMosaicity.split()
fBeamX = float(listStringBeamDistanceMosaicity[3])
fBeamY = float(listStringBeamDistanceMosaicity[5])
xsDataLabelitScreenOutput.setBeamCentreX(XSDataLength(fBeamX))
xsDataLabelitScreenOutput.setBeamCentreY(XSDataLength(fBeamY))
fDistance = float(listStringBeamDistanceMosaicity[7])
xsDataLabelitScreenOutput.setDistance(XSDataLength(fDistance))
fMosaicity = float(listStringBeamDistanceMosaicity[11])
xsDataLabelitScreenOutput.setMosaicity(XSDataAngle(fMosaicity))
iIndex += 3
bContinue = True
bFoundSelectedSolution = False
while (bContinue):
xsDataLabelitScreenSolution = XSDataLabelitScreenSolution()
strLabelitSolution = listLogLines[ iIndex ]
listStringLabelitSolution = strLabelitSolution.split()
if listStringLabelitSolution[0] == ":)" :
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(True))
else:
xsDataLabelitScreenSolution.setHappy(XSDataBoolean(False))
iSolutionNumber = int(listStringLabelitSolution[1])
xsDataLabelitScreenSolution.setSolutionNumber(XSDataInteger(iSolutionNumber))
fMetricFitValue = float(listStringLabelitSolution[2])
xsDataLabelitScreenSolution.setMetricFitValue(XSDataDouble(fMetricFitValue))
strMetricFitCode = listStringLabelitSolution[3]
xsDataLabelitScreenSolution.setMetricFitCode(XSDataString(strMetricFitCode))
fRMSD = float(listStringLabelitSolution[4])
xsDataLabelitScreenSolution.setRmsd(XSDataLength(fRMSD))
iNumberOfSpots = int(listStringLabelitSolution[5])
xsDataLabelitScreenSolution.setNumberOfSpots(XSDataInteger(iNumberOfSpots))
xsDataLabelitScreenSolution.setCrystalSystem(XSDataString(listStringLabelitSolution[6]))
xsDataLabelitScreenSolution.setBravaisLattice(XSDataString(listStringLabelitSolution[7]))
xsDataCell = XSDataCell()
xsDataCell.setLength_a(XSDataLength(float(listStringLabelitSolution[ 8])))
xsDataCell.setLength_b(XSDataLength(float(listStringLabelitSolution[ 9])))
xsDataCell.setLength_c(XSDataLength(float(listStringLabelitSolution[10])))
xsDataCell.setAngle_alpha(XSDataAngle(float(listStringLabelitSolution[11])))
xsDataCell.setAngle_beta(XSDataAngle(float(listStringLabelitSolution[12])))
xsDataCell.setAngle_gamma(XSDataAngle(float(listStringLabelitSolution[13])))
xsDataLabelitScreenSolution.setUnitCell(xsDataCell)
iVolume = int(listStringLabelitSolution[14])
xsDataLabelitScreenSolution.setVolume(XSDataInteger(iVolume))
# Find the selected solution
if (bFoundSelectedSolution == False):
if (xsDataLabelitScreenSolution.getHappy().getValue() == True):
xsDataLabelitScreenOutput.setSelectedSolutionNumber(XSDataInteger(iSolutionNumber))
bFoundSelectedSolution = True
xsDataLabelitScreenOutput.addLabelitScreenSolution(xsDataLabelitScreenSolution)
if (iIndex < (len(listLogLines) - 2)):
iIndex += 1
else:
bContinue = False
return xsDataLabelitScreenOutput