def testGetOutputDataFromDNATableFile(self):
edPluginRdfit = self.createPlugin()
strPathToTableFile = os.path.join(self.strDataPath, "rdfit.xml")
xsDataResultRdfit = edPluginRdfit.getOutputDataFromDNATableFile(strPathToTableFile)
strPathToReference = os.path.join(self.strDataPath, "XSDataResultRdfit_reference.xml")
xsDataResultRdfitReference = XSDataResultRdfit.parseFile(strPathToReference)
EDAssert.equal(xsDataResultRdfitReference.marshal(), xsDataResultRdfit.marshal(), "Test parsing result 'DNA' xml file")
def testGetOutputDataFromDNATableFile(self):
edPluginRdfit = self.createPlugin()
strPathToTableFile = os.path.join(self.strDataPath, "rdfit.xml")
xsDataResultRdfit = edPluginRdfit.getOutputDataFromDNATableFile(strPathToTableFile)
strPathToReference = os.path.join(self.strDataPath, "XSDataResultRdfit_reference.xml")
xsDataResultRdfitReference = XSDataResultRdfit.parseFile(strPathToReference)
EDAssert.equal(xsDataResultRdfitReference.marshal(), xsDataResultRdfit.marshal(), "Test parsing result 'DNA' xml file")
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputRdfit)
self.setDataOutput(XSDataResultRdfit())
self.strScaleIntensityGleFile = self.getBaseName(
) + "_scaleIntensity.gle"
self.strScaleIntensityPlot = self.strScaleIntensityGleFile.replace(
".gle", ".png")
self.strBFactorGleFile = self.getBaseName() + "_bFactor.gle "
self.strBFactorPlot = self.strBFactorGleFile.replace(".gle", ".png")
self.strHtmlPath = self.getBaseName() + ".html"
def getOutputDataFromDNATableFile(self, _strFileName):
"""Parses the result 'DNA'-type XML file"""
xsDataResultRdfit = XSDataResultRdfit()
strDnaTablesXML = self.readProcessFile(_strFileName)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
# Loop through all the tables and fill in the relevant parts of xsDataResultBest
xsDataRDFIT_Results = EDUtilsTable.getTableListFromTables(xsDataDnaTables, "RDFIT_Results")[0]
xsDataListGeneral = EDUtilsTable.getListsFromTable(xsDataRDFIT_Results, "general")[0]
xsDataItemBeta = EDUtilsTable.getItemFromList(xsDataListGeneral, "beta")
if xsDataItemBeta is not None:
beta = xsDataItemBeta.getValueOf_()
xsDataResultRdfit.setBeta(XSDataDouble(beta))
xsDataItemGama = EDUtilsTable.getItemFromList(xsDataListGeneral, "gama")
if xsDataItemGama is not None:
gama = xsDataItemGama.getValueOf_()
xsDataResultRdfit.setGama(XSDataDouble(gama))
xsDataItemDose_half_th = EDUtilsTable.getItemFromList(xsDataListGeneral, "Dose_1/2_th")
if xsDataItemDose_half_th is not None:
dose_half_th = xsDataItemDose_half_th.getValueOf_()
xsDataResultRdfit.setDose_half_th(XSDataDouble(dose_half_th))
xsDataItemDose_half = EDUtilsTable.getItemFromList(xsDataListGeneral, "Dose_1/2")
if xsDataItemDose_half is not None:
dose_half = xsDataItemDose_half.getValueOf_()
xsDataResultRdfit.setDose_half(XSDataDouble(dose_half))
xsDataItemRelative_radiation_sensitivity = EDUtilsTable.getItemFromList(xsDataListGeneral, "Relative_Radiation_Sensitivity")
if xsDataItemRelative_radiation_sensitivity is not None:
relative_radiation_sensitivity = xsDataItemRelative_radiation_sensitivity.getValueOf_()
xsDataResultRdfit.setRelative_radiation_sensitivity(XSDataDouble(relative_radiation_sensitivity))
return xsDataResultRdfit
def getOutputDataFromDNATableFile(self, _strFileName):
"""Parses the result 'DNA'-type XML file"""
xsDataResultRdfit = XSDataResultRdfit()
strDnaTablesXML = self.readProcessFile(_strFileName)
xsDataDnaTables = dna_tables.parseString(strDnaTablesXML)
# Loop through all the tables and fill in the relevant parts of xsDataResultBest
xsDataRDFIT_Results = EDUtilsTable.getTableListFromTables(
xsDataDnaTables, "RDFIT_Results")[0]
xsDataListGeneral = EDUtilsTable.getListsFromTable(
xsDataRDFIT_Results, "general")[0]
xsDataItemBeta = EDUtilsTable.getItemFromList(xsDataListGeneral,
"beta")
if xsDataItemBeta is not None:
beta = xsDataItemBeta.getValueOf_()
xsDataResultRdfit.setBeta(XSDataDouble(beta))
xsDataItemGama = EDUtilsTable.getItemFromList(xsDataListGeneral,
"gama")
if xsDataItemGama is not None:
gama = xsDataItemGama.getValueOf_()
xsDataResultRdfit.setGama(XSDataDouble(gama))
xsDataItemDose_half_th = EDUtilsTable.getItemFromList(
xsDataListGeneral, "Dose_1/2_th")
if xsDataItemDose_half_th is not None:
dose_half_th = xsDataItemDose_half_th.getValueOf_()
xsDataResultRdfit.setDose_half_th(XSDataDouble(dose_half_th))
xsDataItemDose_half = EDUtilsTable.getItemFromList(
xsDataListGeneral, "Dose_1/2")
if xsDataItemDose_half is not None:
dose_half = xsDataItemDose_half.getValueOf_()
xsDataResultRdfit.setDose_half(XSDataDouble(dose_half))
xsDataItemRelative_radiation_sensitivity = EDUtilsTable.getItemFromList(
xsDataListGeneral, "Relative_Radiation_Sensitivity")
if xsDataItemRelative_radiation_sensitivity is not None:
relative_radiation_sensitivity = xsDataItemRelative_radiation_sensitivity.getValueOf_(
)
xsDataResultRdfit.setRelative_radiation_sensitivity(
XSDataDouble(relative_radiation_sensitivity))
return xsDataResultRdfit
