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 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 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 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 doSuccessActionCharacterisation(self, _edPlugin):
"""
retrieve the potential warning messages
"""
EDPluginControlInterfacev1_1.doSuccessActionCharacterisation(
self, _edPlugin)
# Generate file with executive summary...
pyStrCharacterisationExecutiveSummary = ""
pyListExecutiveSummaryLines = self.getPluginCharacterisation(
).getListExecutiveSummaryLines()
for pyStrLine in pyListExecutiveSummaryLines:
pyStrCharacterisationExecutiveSummary += pyStrLine + "\n"
pyStrSummaryDirectory = self.getWorkingDirectory()
pyStrSummaryPath = os.path.join(
pyStrSummaryDirectory, "CharacterisationExecutiveSummary.txt")
EDUtilsFile.writeFile(pyStrSummaryPath,
pyStrCharacterisationExecutiveSummary)
xsDataResultCCP4i = XSDataResultCCP4i()
# Construct the listOfOutputFiles string...
pyStrListOfOutputFiles = '\n'
pyStrListOfOutputFiles = pyStrListOfOutputFiles + self.getBaseDirectory(
) + '\n'
xsDataOutput = self.getPluginCharacterisation().getDataOutput()
pyListPredictionImages = xsDataOutput.getIndexingResult(
).getPredictionResult().getPredictionImage()
for xsDataImagePrediction in pyListPredictionImages:
strImagePath = xsDataImagePrediction.getPath().getValue()
pyStrListOfOutputFiles = pyStrListOfOutputFiles + strImagePath + '\n'
pyStrCharacterisationDirectory = os.path.join(
self.getWorkingDirectory(), "Characterisation")
# "Hack" for determining if we use version 1.1 or 1.2 of the BEST plugin...
pyStrBestWorkingDirectory = os.path.join(
pyStrCharacterisationDirectory, "Strategy")
pyStrBestPlotFilePath = None
pyStrBestLogFilePath = None
if (os.path.exists(os.path.join(pyStrBestWorkingDirectory,
"Bestv1_1"))):
pyStrBestWorkingDirectory = os.path.join(pyStrBestWorkingDirectory,
"Bestv1_1")
pyStrBestPlotFilePath = os.path.join(pyStrBestWorkingDirectory,
"Bestv1_1_plots.mtv")
pyStrBestLogFilePath = os.path.join(pyStrBestWorkingDirectory,
"Bestv1_1.log")
elif (os.path.exists(
os.path.join(pyStrBestWorkingDirectory, "Bestv1_2"))):
pyStrBestWorkingDirectory = os.path.join(pyStrBestWorkingDirectory,
"Bestv1_2")
pyStrBestPlotFilePath = os.path.join(pyStrBestWorkingDirectory,
"Bestv1_2_plots.mtv")
pyStrBestLogFilePath = os.path.join(pyStrBestWorkingDirectory,
"best.log")
pyStrCharacterisationOutput = None
if self.getPluginCharacterisation().getClassName(
) == "EDPluginControlCharacterisationv1_1":
pyStrCharacterisationOutput = os.path.join(
pyStrCharacterisationDirectory,
"ControlCharacterisationv1_1_dataOutput.xml")
elif self.getPluginCharacterisation().getClassName(
) == "EDPluginControlCharacterisationv1_2":
pyStrCharacterisationOutput = os.path.join(
pyStrCharacterisationDirectory,
"ControlCharacterisationv1_2_dataOutput.xml")
pyStrListOfOutputFiles = pyStrListOfOutputFiles + pyStrCharacterisationOutput + '\n'
if (pyStrBestLogFilePath is not None):
pyStrListOfOutputFiles = pyStrListOfOutputFiles + pyStrBestLogFilePath + '\n'
pyStrListOfOutputFiles = pyStrListOfOutputFiles + pyStrBestPlotFilePath + '\n'
pyStrListOfOutputFiles = pyStrListOfOutputFiles + pyStrSummaryPath + '\n'
xsDataStringListOfOutputFiles = XSDataString(pyStrListOfOutputFiles)
xsDataResultCCP4i.setListOfOutputFiles(xsDataStringListOfOutputFiles)
self.setDataOutput(xsDataResultCCP4i)
