def testExecute(self):
self.run()
# Compare results
strXMLExpected = self.readAndParseFile(self.__strReferenceDataOutputFile)
xsDataObtained = self.getPlugin().getDataOutput()
xsDataExpected = XSDataMOSFLMOutputIntegration.parseString(strXMLExpected)
# Remove the bestFileHKL part which creates problem...
xsDataObtained.setBestfileHKL(None)
xsDataExpected.setBestfileHKL(None)
EDAssert.strAlmostEqual(xsDataExpected.marshal(), xsDataObtained.marshal(), "(MOSFLM integration result comparison - expected versus obtained)", 0.1, 5000)
def testGenerateExecutiveSummary(self):
pluginIntegration = self.createPlugin()
pluginIntegration.setScriptExecutable("cat")
pluginIntegration.configure()
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
strMOSFLMInputIntegrationXML = self.readAndParseFile(self.strReferenceDataInputFile)
strMOSFLMOutputIntegrationXML = self.readAndParseFile(self.strReferenceDataOutputFile)
xsDataMOSFLMInputIntegration = XSDataMOSFLMInputIntegration.parseString(strMOSFLMInputIntegrationXML)
xsDataMOSFLMOutputIntegration = XSDataMOSFLMOutputIntegration.parseString(strMOSFLMOutputIntegrationXML)
pluginIntegration.setDataInput(xsDataMOSFLMInputIntegration)
pluginIntegration.setDataOutput(xsDataMOSFLMOutputIntegration)
pluginIntegration.generateExecutiveSummary(pluginIntegration)
pluginIntegration.verboseScreenExecutiveSummary()
self.cleanUp(pluginIntegration)
def testGenerateXSDataIntegrationSubWedgeResult(self):
strFilename = "XSDataMOSFLMOutputIntegration_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLMOSFLMOutputIntegration = EDUtilsTest.readAndParseFile(strPath)
from XSDataMOSFLMv10 import XSDataMOSFLMOutputIntegration
xsDataMOSFLMOutputIntegration = XSDataMOSFLMOutputIntegration.parseString(strXMLMOSFLMOutputIntegration)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIntegrationSubWedgeResult = EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationSubWedgeResult(xsDataMOSFLMOutputIntegration)
strReferenceFilename = "XSDataIntegrationSubWedgeResult_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath, strReferenceFilename)
strXMLIntegrationSubWedgeReference = EDUtilsTest.readAndParseFile(strReferencePath)
from XSDataMXv1 import XSDataIntegrationSubWedgeResult
xsDataIntegrationSubWedgeResult = XSDataIntegrationSubWedgeResult.parseString(strXMLIntegrationSubWedgeReference)
EDAssert.equal(xsDataIntegrationSubWedgeResult.marshal(), xsDataIntegrationSubWedgeResult.marshal())
def testExecute(self):
self.run()
# Compare results
strXMLExpected = self.readAndParseFile(
self.__strReferenceDataOutputFile)
xsDataObtained = self.getPlugin().getDataOutput()
xsDataExpected = XSDataMOSFLMOutputIntegration.parseString(
strXMLExpected)
# Remove the bestFileHKL part which creates problem...
xsDataObtained.setBestfileHKL(None)
xsDataExpected.setBestfileHKL(None)
EDAssert.strAlmostEqual(
xsDataExpected.marshal(), xsDataObtained.marshal(),
"(MOSFLM integration result comparison - expected versus obtained)",
0.1, 5000)
def testCreateDataMOSFLMOutputIntegration(self):
pluginIntegration = self.createPlugin()
pluginIntegration.setScriptExecutable("cat")
pluginIntegration.configure()
strBaseName = pluginIntegration.getBaseName()
shutil.copyfile(
os.path.join(self.strUnitTestDataHome,
"EDPluginMOSFLMIntegrationv10_bestfileDat_ok.txt"),
os.path.join(pluginIntegration.getWorkingDirectory(),
"bestfile.dat"))
shutil.copyfile(
os.path.join(self.strUnitTestDataHome,
"EDPluginMOSFLMIntegrationv10_bestfilePar_ok.txt"),
os.path.join(pluginIntegration.getWorkingDirectory(),
"bestfile.par"))
shutil.copyfile(
os.path.join(self.strUnitTestDataHome,
"EDPluginMOSFLMIntegrationv10_bestfileHKL_ok.txt"),
os.path.join(pluginIntegration.getWorkingDirectory(),
"bestfile.hkl"))
shutil.copyfile(
os.path.join(
self.strUnitTestDataHome,
"EDPluginMOSFLMIntegrationv10_outputDnaTables_ok.xml"),
os.path.join(pluginIntegration.getWorkingDirectory(),
strBaseName + "_dnaTables.xml"))
strMatrixFile = os.path.join(self.strUnitTestDataHome,
"EDPluginMOSFLMv10_autoindexMat_ok.txt")
pluginIntegration.setMatrixFileName(strMatrixFile)
xsDataMOSFLMIntegrationOutput = pluginIntegration.createDataMOSFLMOutputIntegration(
)
# Fix problem with absolute path by replacing it with a fixed one
xsDataFile = XSDataFile()
xsDataFile.setPath(
XSDataString("/tmp/EDPluginMOSFLMIntegrationv10_process_1_1.mtz"))
xsDataMOSFLMIntegrationOutput.setGeneratedMTZFile(xsDataFile)
strReferenceXML = self.readAndParseFile(
self.strReferenceDataOutputFile)
xsDataMOSFLMIntegrationOutputReference = XSDataMOSFLMOutputIntegration.parseString(
strReferenceXML)
# Replace path to log file since it cannot be determined by the unit test
xsDataMOSFLMIntegrationOutput.setPathToLogFile(
XSDataFile(XSDataString("MOSFLMIntegrationv10.log")))
EDAssert.equal(xsDataMOSFLMIntegrationOutputReference.marshal(),
xsDataMOSFLMIntegrationOutput.marshal())
def testGenerateExecutiveSummary(self):
pluginIntegration = self.createPlugin()
pluginIntegration.setScriptExecutable("cat")
pluginIntegration.configure()
from XSDataMOSFLMv10 import XSDataMOSFLMInputIntegration
strMOSFLMInputIntegrationXML = self.readAndParseFile(
self.strReferenceDataInputFile)
strMOSFLMOutputIntegrationXML = self.readAndParseFile(
self.strReferenceDataOutputFile)
xsDataMOSFLMInputIntegration = XSDataMOSFLMInputIntegration.parseString(
strMOSFLMInputIntegrationXML)
xsDataMOSFLMOutputIntegration = XSDataMOSFLMOutputIntegration.parseString(
strMOSFLMOutputIntegrationXML)
pluginIntegration.setDataInput(xsDataMOSFLMInputIntegration)
pluginIntegration.setDataOutput(xsDataMOSFLMOutputIntegration)
pluginIntegration.generateExecutiveSummary(pluginIntegration)
pluginIntegration.verboseScreenExecutiveSummary()
self.cleanUp(pluginIntegration)
def testCreateDataMOSFLMOutputIntegration(self):
pluginIntegration = self.createPlugin()
pluginIntegration.setScriptExecutable("cat")
pluginIntegration.configure()
strBaseName = pluginIntegration.getBaseName()
shutil.copyfile(os.path.join(self.strUnitTestDataHome, "EDPluginMOSFLMIntegrationv10_bestfileDat_ok.txt"), os.path.join (pluginIntegration.getWorkingDirectory(), "bestfile.dat"))
shutil.copyfile(os.path.join(self.strUnitTestDataHome, "EDPluginMOSFLMIntegrationv10_bestfilePar_ok.txt"), os.path.join (pluginIntegration.getWorkingDirectory(), "bestfile.par"))
shutil.copyfile(os.path.join(self.strUnitTestDataHome, "EDPluginMOSFLMIntegrationv10_bestfileHKL_ok.txt"), os.path.join (pluginIntegration.getWorkingDirectory(), "bestfile.hkl"))
shutil.copyfile(os.path.join(self.strUnitTestDataHome, "EDPluginMOSFLMIntegrationv10_outputDnaTables_ok.xml"), os.path.join(pluginIntegration.getWorkingDirectory(), strBaseName + "_dnaTables.xml"))
strMatrixFile = os.path.join(self.strUnitTestDataHome, "EDPluginMOSFLMv10_autoindexMat_ok.txt")
pluginIntegration.setMatrixFileName(strMatrixFile)
xsDataMOSFLMIntegrationOutput = pluginIntegration.createDataMOSFLMOutputIntegration()
# Fix problem with absolute path by replacing it with a fixed one
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString("/tmp/EDPluginMOSFLMIntegrationv10_process_1_1.mtz"))
xsDataMOSFLMIntegrationOutput.setGeneratedMTZFile(xsDataFile)
strReferenceXML = self.readAndParseFile(self.strReferenceDataOutputFile)
xsDataMOSFLMIntegrationOutputReference = XSDataMOSFLMOutputIntegration.parseString(strReferenceXML)
EDAssert.equal(xsDataMOSFLMIntegrationOutputReference.marshal(), xsDataMOSFLMIntegrationOutput.marshal())
def testGenerateXSDataIntegrationSubWedgeResult(self):
strFilename = "XSDataMOSFLMOutputIntegration_reference.xml"
strPath = os.path.join(self.m_strDataPath, strFilename)
strXMLMOSFLMOutputIntegration = EDUtilsTest.readAndParseFile(strPath)
from XSDataMOSFLMv10 import XSDataMOSFLMOutputIntegration
xsDataMOSFLMOutputIntegration = XSDataMOSFLMOutputIntegration.parseString(
strXMLMOSFLMOutputIntegration)
from EDHandlerXSDataMOSFLMv10 import EDHandlerXSDataMOSFLMv10
xsDataIntegrationSubWedgeResult = EDHandlerXSDataMOSFLMv10.generateXSDataIntegrationSubWedgeResult(
xsDataMOSFLMOutputIntegration)
strReferenceFilename = "XSDataIntegrationSubWedgeResult_reference.xml"
strReferencePath = os.path.join(self.m_strDataPath,
strReferenceFilename)
strXMLIntegrationSubWedgeReference = EDUtilsTest.readAndParseFile(
strReferencePath)
from XSDataMXv1 import XSDataIntegrationSubWedgeResult
xsDataIntegrationSubWedgeResult = XSDataIntegrationSubWedgeResult.parseString(
strXMLIntegrationSubWedgeReference)
EDAssert.equal(xsDataIntegrationSubWedgeResult.marshal(),
xsDataIntegrationSubWedgeResult.marshal())
