def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
"""
"""
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
from XSDataCommon import XSDataString
from XSDataCommon import XSDataFloat
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
from XSDataMXv1 import XSDataCell
from XSDataMXv1 import XSDataSpaceGroup
edPluginStrategy = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.strDataPath, "XSConfiguration_ESRF.xml"))
edPluginStrategy.setConfiguration(xsPluginItemGood01)
edPluginStrategy.configure()
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataChain.setNumberOfMonomers(XSDataFloat(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
EDAssert.equal(3, updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getNumberOf().getValue())
EDAssert.equal("S", updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue())
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataChain.setNumberOfMonomers(XSDataFloat(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataFloat(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
EDVerbose.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if(heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def testGenerateStrategyShortSummary(self):
edPluginStrategy = self.createPlugin()
strReferenceOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataResultStrategy_2_sweep.xml")
strXML = self.readAndParseFile(strReferenceOutputFile)
xsDataStrategyResult = XSDataResultStrategy.parseString(strXML)
edPluginStrategy.generateStrategyShortSummary(xsDataStrategyResult)
for strLine in edPluginStrategy.getDataOutput("strategyShortSummary")[0].getValue().split("\n"):
EDVerbose.unitTest(strLine)
def testGenerateStrategyShortSummary(self):
edPluginStrategy = self.createPlugin()
strReferenceOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataResultStrategy_2_sweep.xml")
strXML = self.readAndParseFile(strReferenceOutputFile)
xsDataStrategyResult = XSDataResultStrategy.parseString(strXML)
edPluginStrategy.generateStrategyShortSummary(xsDataStrategyResult)
for strLine in edPluginStrategy.getDataOutput("strategyShortSummary")[0].getValue().split("\n"):
EDVerbose.unitTest(strLine)
def testGenerateIntegrationShortSummary(self):
edPluginControlIntegrationv10 = self.createPlugin()
strReferenceOutputFile = os.path.join(self.getPluginTestsDataHome(), "XSDataIntegrationResult_reference.xml")
strXML = self.readAndParseFile(strReferenceOutputFile)
xsDataIntegrationResult = XSDataIntegrationResult.parseString(strXML)
edPluginControlIntegrationv10.generateIntegrationShortSummary(xsDataIntegrationResult)
for strLine in edPluginControlIntegrationv10.getDataOutput("integrationShortSummary")[0].getValue().split("\n"):
EDVerbose.unitTest(strLine)
def postProcess(self):
# try to remove any created directories in /tmp
listFilesTmp = os.listdir("/tmp")
for strFile in listFilesTmp:
if strFile.startswith("EDNA2html.log"):
try:
os.remove(os.path.join("/tmp", strFile))
except:
EDVerbose.unitTest("Couldn't delete temporary file: %s" % strFile)
def postProcess(self):
# try to remove any created directories in /tmp
listFilesTmp = os.listdir("/tmp")
for strFile in listFilesTmp:
if strFile.startswith("EDNA2html.log"):
try:
os.remove(os.path.join("/tmp", strFile))
except:
EDVerbose.unitTest("Couldn't delete temporary file: %s" %
strFile)
def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
from XSDataCommon import XSDataString
from XSDataCommon import XSDataFloat
from XSDataMXv1 import XSDataStructure
from XSDataMXv1 import XSDataChain
from XSDataMXv1 import XSDataAtom
from XSDataMXv1 import XSDataLigand
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataChemicalCompositionMM
from XSDataMXv1 import XSDataAtomicComposition
from XSDataMXv1 import XSDataSolvent
from XSDataMXv1 import XSDataCell
from XSDataMXv1 import XSDataSpaceGroup
edPluginStrategy = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.strDataPath, "XSConfiguration_ESRF.xml"))
edPluginStrategy.setConfiguration(xsPluginItemGood01)
edPluginStrategy.configure()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataChain.setNumberOfMonomers(XSDataFloat(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
EDAssert.equal(3, updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getNumberOf().getValue())
EDAssert.equal("S", updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue())
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataChain.setNumberOfMonomers(XSDataFloat(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataFloat(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
EDVerbose.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if(heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def unitTestDetectNumberOfCPUs(self):
"""
test the execution of detectNumberOfCPUs
"""
iNbCPU = EDUtilsParallel.detectNumberOfCPUs()
EDVerbose.unitTest("Detection of the number of Cores: %s" % iNbCPU)
EDAssert.equal(types.IntType, type(iNbCPU), "Number of CPU is an integer")
iNbCPU = EDUtilsParallel.detectNumberOfCPUs(1) #limited to 1
EDAssert.equal(1, iNbCPU, "Limit number of CPU")
iNbCPU = EDUtilsParallel.detectNumberOfCPUs(100, True) #forced to 100
EDAssert.equal(100, iNbCPU, "Force number of CPU")
def unitTestDetectNumberOfCPUs(self):
"""
test the execution of detectNumberOfCPUs
"""
iNbCPU = EDUtilsParallel.detectNumberOfCPUs()
EDVerbose.unitTest("Detection of the number of Cores: %s" % iNbCPU)
EDAssert.equal(types.IntType, type(iNbCPU),
"Number of CPU is an integer")
iNbCPU = EDUtilsParallel.detectNumberOfCPUs(1) #limited to 1
EDAssert.equal(1, iNbCPU, "Limit number of CPU")
iNbCPU = EDUtilsParallel.detectNumberOfCPUs(100, True) #forced to 100
EDAssert.equal(100, iNbCPU, "Force number of CPU")
def loadTestImage(self, _listImageFileName):
"""
This method checks the presence of all the images in the list of image file names
in the $EDNA_HOME/tests/data/images directory. If one image is not present
this method tries to download it from http://www.edna-site.org/data/tests/images
"""
if not os.path.isdir(EDUtilsPath.EDNA_TESTIMAGES):
os.makedirs(EDUtilsPath.EDNA_TESTIMAGES)
for strImageName in _listImageFileName:
strImagePath = os.path.join(EDUtilsPath.EDNA_TESTIMAGES,
strImageName)
if (not os.path.exists(strImagePath)):
EDVerbose.unitTest(
"Trying to download image %s, timeout set to %d s" %
(strImagePath, iMAX_DOWNLOAD_TIME))
if "http_proxy" in os.environ:
dictProxies = {'http': os.environ["http_proxy"]}
proxy_handler = urllib2.ProxyHandler(dictProxies)
opener = urllib2.build_opener(proxy_handler).open
else:
opener = urllib2.urlopen
# Nota: since python2.6 there is a timeout in the urllib2
timer = threading.Timer(iMAX_DOWNLOAD_TIME + 1,
timeoutDuringDownload)
timer.start()
if sys.version > (2, 6):
data = opener("%s/%s" % (self.URL_EDNA_SITE, strImageName),
data=None,
timeout=iMAX_DOWNLOAD_TIME).read()
else:
data = opener("%s/%s" % (self.URL_EDNA_SITE, strImageName),
data=None).read()
timer.cancel()
try:
open(strImagePath, "wb").write(data)
except IOError:
raise IOError(
"unable to write downloaded data to disk at %s" %
strImagePath)
if os.path.exists(strImagePath):
EDVerbose.unitTest("Image %s successfully downloaded." %
strImagePath)
else:
raise RuntimeError(
"Could not automatically download test images %r! \n \
If you are behind a firewall, please set the environment variable http_proxy. \n \
Otherwise please try to download the images manually from \n \
http://www.edna-site.org/data/tests/images"
% _listImageFileName)
def run(self):
"""
Executes the plugin and checks that the data output is not None
"""
EDVerbose.DEBUG("EDTestCasePluginExecute: Executing " + self.getPluginName())
self._edPlugin.executeSynchronous()
# Check that the plugin didn't end in failure
EDAssert.equal(self._bAcceptPluginFailure , self._edPlugin.isFailure(), \
"Plugin failure assert: should be %r, was %r" % (self._bAcceptPluginFailure , self._edPlugin.isFailure()))
# Checks the number of error messages
EDAssert.equal(self._iNoExpectedErrorMessages, len(self._edPlugin.getListOfErrorMessages()), \
"Number of error messages: expected %d, got %d" % (self._iNoExpectedErrorMessages, len(self._edPlugin.getListOfErrorMessages())))
# Checks the number of warning messages
EDAssert.equal(self._iNoExpectedWarningMessages, len(self._edPlugin.getListOfWarningMessages()), \
"Number of warning messages: expected %d, got %d" % (self._iNoExpectedWarningMessages, len(self._edPlugin.getListOfWarningMessages())))
# Check the output data
listOfDataOutputKeys = self._edPlugin.getListOfDataOutputKeys()
for strReferenceOutputDataKey in self._dictStrReferenceDataOutputFiles.keys():
# Only check the reference data keys
if (strReferenceOutputDataKey in listOfDataOutputKeys):
EDVerbose.unitTest("Testing data output for %s" % strReferenceOutputDataKey)
listReferenceFile = self._dictStrReferenceDataOutputFiles[ strReferenceOutputDataKey ]
if (type(listReferenceFile) != types.ListType):
listReferenceFile = [ listReferenceFile ]
listReferenceOutput = []
for strReferenceFile in listReferenceFile:
listReferenceOutput.append(self.readAndParseFile(strReferenceFile))
# Obtained output
listObtainedOutputXML = []
pyObjectObtainedDataOutput = self._edPlugin.getDataOutput(strReferenceOutputDataKey)
listObtainedOutput = None
if (type(pyObjectObtainedDataOutput) == types.ListType):
listObtainedOutput = pyObjectObtainedDataOutput
else:
listObtainedOutput = [ pyObjectObtainedDataOutput ]
for xsDataOutput in listObtainedOutput:
listObtainedOutputXML.append(xsDataOutput.marshal())
# Compare the lists, sort them first
listReferenceOutput.sort()
listObtainedOutputXML.sort()
for iIndex in range(len(listReferenceOutput)):
# Check of deprecated tests - if default data key only warn
if (strReferenceOutputDataKey == self._strDefaultOutputDataKey):
if (listReferenceOutput[ iIndex ] != listObtainedOutputXML[ iIndex ]):
EDVerbose.unitTest("WARNING! Expected output is not corresponding to obtained output.")
else:
EDAssert.equal(listReferenceOutput[ iIndex ], listObtainedOutputXML[ iIndex ])
# Legacy - save output data
if (strReferenceOutputDataKey == self._strDefaultOutputDataKey):
if (self.m_edObtainedOutputDataFile is None):
self.m_edObtainedOutputDataFile = self.getPluginName() + "_output.xml"
EDUtilsFile.writeFile(self.m_edObtainedOutputDataFile, self._edPlugin.getDataOutput().marshal())
def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
edPluginStrategy = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.strDataPath, "XSConfiguration_ESRF.xml"))
edPluginStrategy.setConfiguration(xsPluginItemGood01)
edPluginStrategy.configure()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
EDAssert.equal(
3,
updatedChemicalComposition.getStructure()
.getChain()[0]
.getHeavyAtoms()
.getAtom()[0]
.getNumberOf()
.getValue(),
)
EDAssert.equal(
"S",
updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue(),
)
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
EDVerbose.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if heavyAtom.getSymbol().getValue() == "S":
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def testExecute(self):
self.run()
# Checks that there are no error messages
edPlugin = self.getPlugin()
# Checks some parts of the result
xsDataIntegrationResultObtained = edPlugin.getDataOutput()
# Check that we have at least the best files in each integration subwedge
for xsDataIntegrationSubWedgeResult in xsDataIntegrationResultObtained.getIntegrationSubWedgeResult():
if ((xsDataIntegrationSubWedgeResult.getBestfileDat() is None) or \
(xsDataIntegrationSubWedgeResult.getBestfilePar() is None) or \
(xsDataIntegrationSubWedgeResult.getBestfileHKL() is None)):
EDVerbose.unitTest("Missing BEST output data in the integration subwedge results!")
EDAssert.equal(True, False)
def testExecute(self):
self.run()
# Checks that there are no error messages
edPlugin = self.getPlugin()
# Checks some parts of the result
xsDataIntegrationResultObtained = edPlugin.getDataOutput()
# Check that we have at least the best files in each integration subwedge
for xsDataIntegrationSubWedgeResult in xsDataIntegrationResultObtained.getIntegrationSubWedgeResult(
):
if ((xsDataIntegrationSubWedgeResult.getBestfileDat() is None) or \
(xsDataIntegrationSubWedgeResult.getBestfilePar() is None) or \
(xsDataIntegrationSubWedgeResult.getBestfileHKL() is None)):
EDVerbose.unitTest(
"Missing BEST output data in the integration subwedge results!"
)
EDAssert.equal(True, False)
def processKernel(self):
"""
This method executes the test suite.
"""
EDVerbose.DEBUG("Execution: EDTestSuite.processKernel()")
EDVerbose.screen("")
EDVerbose.screen("")
EDVerbose.unitTest("###################################################################")
EDVerbose.unitTest("STARTING::" + self.getTestName())
EDVerbose.unitTest("###################################################################")
self.setTimeInit()
for edTestCase in self.__listTestCase:
edTestCase.execute()
if edTestCase.isExecuted():
self.__iNumberTestMethodSuccess += edTestCase.getNumberTestMethodSuccess()
if edTestCase.getNumberTestMethodFailure() == 0:
self.__iNumberTestCaseSuccess += 1
else:
self.__iNumberTestCaseFailure += 1
self.__iNumberTestMethodFailure += edTestCase.getNumberTestMethodFailure()
self.__dictTestCaseFailureMessages[edTestCase.getClassName()] = edTestCase.getMethodFailureMessages()
else:
self.__dictTestCaseNotExecuted[edTestCase.getClassName()] = edTestCase.getReasonForNotBeingExectuted()
EDVerbose.screen()
for edTestSuite in self.__listTestSuite:
edTestSuite.execute()
self.__iNumberTestSuite += 1
self.__iNumberTestMethodSuccess += edTestSuite.getNumberTestMethodSuccess()
self.__iNumberTestMethodFailure += edTestSuite.getNumberTestMethodFailure()
self.__iNumberTestCaseSuccess += edTestSuite.getNumberTestCaseSuccess()
self.__iNumberTestCaseFailure += edTestSuite.getNumberTestCaseFailure()
self.extendDictionary(self.__dictTestCaseNotExecuted, edTestSuite.getDictTestCaseNotExecuted())
self.extendDictionary(self.__dictTestSuiteNotExecuted, edTestSuite.getDictTestSuiteNotExecuted())
self.extendDictionary(self.__dictTestCaseFailureMessages, edTestSuite.getDictTestCaseFailureMessages())
self.setTimeEnd()
def loadTestImage(self, _listImageFileName):
"""
This method checks the presence of all the images in the list of image file names
in the $EDNA_HOME/tests/data/images directory. If one image is not present
this method tries to download it from http://www.edna-site.org/data/tests/images
"""
if not os.path.isdir(EDUtilsPath.EDNA_TESTIMAGES):
os.makedirs(EDUtilsPath.EDNA_TESTIMAGES)
for strImageName in _listImageFileName:
strImagePath = os.path.join(EDUtilsPath.EDNA_TESTIMAGES, strImageName)
if(not os.path.exists(strImagePath)):
EDVerbose.unitTest("Trying to download image %s, timeout set to %d s" % (strImagePath, iMAX_DOWNLOAD_TIME))
if os.environ.has_key("http_proxy"):
dictProxies = {'http': os.environ["http_proxy"]}
proxy_handler = urllib2.ProxyHandler(dictProxies)
opener = urllib2.build_opener(proxy_handler).open
else:
opener = urllib2.urlopen
# Nota: since python2.6 there is a timeout in the urllib2
timer = threading.Timer(iMAX_DOWNLOAD_TIME + 1, timeoutDuringDownload)
timer.start()
if sys.version > (2, 6):
data = opener("%s/%s" % (self.URL_EDNA_SITE, strImageName), data=None, timeout=iMAX_DOWNLOAD_TIME).read()
else:
data = opener("%s/%s" % (self.URL_EDNA_SITE, strImageName), data=None).read()
timer.cancel()
try:
open(strImagePath, "wb").write(data)
except IOError:
raise IOError, "unable to write downloaded data to disk at %s" % strImagePath
if os.path.exists(strImagePath):
EDVerbose.unitTest("Image %s successfully downloaded." % strImagePath)
else:
raise RuntimeError, "Could not automatically download test images %r! \n \
If you are behind a firewall, please set the environment variable http_proxy. \n \
Otherwise please try to download the images manually from \n \
http://www.edna-site.org/data/tests/images" % _listImageFileName
def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
edPluginStrategy = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.strDataPath, "XSConfiguration_ESRF.xml"))
edPluginStrategy.setConfiguration(xsPluginItemGood01)
edPluginStrategy.configure()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
EDAssert.equal(3, updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getNumberOf().getValue())
EDAssert.equal("S", updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue())
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
EDVerbose.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if(heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def processKernel(self):
"""
This method executes the test suite.
"""
EDVerbose.DEBUG("Execution: EDTestSuite.processKernel()")
EDVerbose.screen("")
EDVerbose.screen("")
EDVerbose.unitTest(
"###################################################################"
)
EDVerbose.unitTest("STARTING::" + self.getTestName())
EDVerbose.unitTest(
"###################################################################"
)
self.setTimeInit()
for edTestCase in self.__listTestCase:
if edTestCase._deactivated:
continue
edTestCase.execute()
if edTestCase._deactivated:
continue
if edTestCase.isExecuted():
self.__iNumberTestMethodSuccess += edTestCase.getNumberTestMethodSuccess(
)
if edTestCase.getNumberTestMethodFailure() == 0:
self.__iNumberTestCaseSuccess += 1
else:
self.__iNumberTestCaseFailure += 1
self.__iNumberTestMethodFailure += edTestCase.getNumberTestMethodFailure(
)
self.__dictTestCaseFailureMessages[edTestCase.getClassName(
)] = edTestCase.getMethodFailureMessages()
else:
self.__dictTestCaseNotExecuted[edTestCase.getClassName(
)] = edTestCase.getReasonForNotBeingExectuted()
EDVerbose.screen()
for edTestSuite in self.__listTestSuite:
edTestSuite.execute()
self.__iNumberTestSuite += 1
self.__iNumberTestMethodSuccess += edTestSuite.getNumberTestMethodSuccess(
)
self.__iNumberTestMethodFailure += edTestSuite.getNumberTestMethodFailure(
)
self.__iNumberTestCaseSuccess += edTestSuite.getNumberTestCaseSuccess(
)
self.__iNumberTestCaseFailure += edTestSuite.getNumberTestCaseFailure(
)
self.extendDictionary(self.__dictTestCaseNotExecuted,
edTestSuite.getDictTestCaseNotExecuted())
self.extendDictionary(self.__dictTestSuiteNotExecuted,
edTestSuite.getDictTestSuiteNotExecuted())
self.extendDictionary(self.__dictTestCaseFailureMessages,
edTestSuite.getDictTestCaseFailureMessages())
self.setTimeEnd()
def postProcess(self):
"""
This method writes out the results of the test suite.
"""
EDVerbose.screen()
EDVerbose.screen()
EDVerbose.unitTest(
"###################################################################"
)
strResult = None
if self.__iNumberTestCaseFailure == 0 and self.__iNumberTestMethodFailure == 0:
strResult = "SUCCESS"
else:
strResult = "FAILURE"
EDVerbose.unitTest("Result for %s : %s" %
(self.getTestName(), strResult))
EDVerbose.unitTest()
if self.__iNumberTestSuite > 0:
EDVerbose.unitTest(
" Number of executed test suites in this test suite : %d" %
self.__iNumberTestSuite)
EDVerbose.unitTest()
if self.__dictTestSuiteNotExecuted != {}:
EDVerbose.unitTest()
EDVerbose.unitTest(
"OBS! The following test suites were not executed due to errors:"
)
EDVerbose.unitTest()
for strTestSuiteName in self.__dictTestSuiteNotExecuted.keys():
EDVerbose.unitTest(
" %s : %s" %
(self.__dictTestSuiteNotExecuted[strTestSuiteName],
strTestSuiteName))
EDVerbose.unitTest()
if self.__dictTestCaseNotExecuted != {}:
EDVerbose.unitTest()
EDVerbose.unitTest(
"OBS! The following test cases not executed due to errors:")
EDVerbose.unitTest()
for strTestCaseName in self.__dictTestCaseNotExecuted.keys():
EDVerbose.unitTest(" %s :" % strTestCaseName)
EDVerbose.unitTest(
" %s" %
self.__dictTestCaseNotExecuted[strTestCaseName])
EDVerbose.unitTest()
EDVerbose.unitTest(
" Total number of test cases NOT EXECUTED : %d" %
len(self.__dictTestCaseNotExecuted))
EDVerbose.unitTest()
if self.__iNumberTestCaseSuccess != 0 or self.__iNumberTestCaseFailure != 0:
EDVerbose.unitTest(
" Total number of test cases executed with SUCCESS : %d" %
self.__iNumberTestCaseSuccess)
EDVerbose.unitTest(
" Total number of test cases executed with FAILURE : %d" %
self.__iNumberTestCaseFailure)
EDVerbose.unitTest()
if self.__dictTestCaseFailureMessages != {}:
EDVerbose.unitTest("")
EDVerbose.unitTest(
"OBS! The following test methods ended with failure:")
EDVerbose.unitTest("")
for strTestCaseName in self.__dictTestCaseFailureMessages.keys():
EDVerbose.unitTest(" %s :" % strTestCaseName)
for strMethodName in self.__dictTestCaseFailureMessages[
strTestCaseName].keys():
EDVerbose.unitTest(" %s :" %
strMethodName.split(".")[1])
EDVerbose.unitTest(
" %s" %
self.__dictTestCaseFailureMessages[strTestCaseName]
[strMethodName])
EDVerbose.unitTest("")
EDVerbose.unitTest("")
if self.__iNumberTestMethodSuccess != 0 or self.__iNumberTestMethodFailure != 0:
EDVerbose.unitTest(
"Total number of test methods executed with SUCCESS : %d" %
self.__iNumberTestMethodSuccess)
EDVerbose.unitTest(
"Total number of test methods executed with FAILURE : %d" %
self.__iNumberTestMethodFailure)
EDVerbose.unitTest()
EDVerbose.unitTest(
" Runtime : %.3f [s]" %
self.getRunTime())
EDVerbose.unitTest(
"###################################################################"
)
def processKernel(self):
"""
Executes the test case.
"""
EDVerbose.DEBUG("EDTestCase.processKernel")
EDVerbose.screen()
EDVerbose.unitTest(
"==================================================================="
)
if self.getTestSuiteName() is not None:
EDVerbose.unitTest("TEST SUITE : %s" % self.getTestSuiteName())
EDVerbose.unitTest("TEST CASE : %s" % self.getClassName())
EDVerbose.unitTest(" ")
if self.__strReasonForNotBeingExecuted == "":
self.setTimeInit()
iNumberMethods = self.getNumberOfTests()
EDVerbose.unitTest("Total number of tests : %d" % iNumberMethods)
EDVerbose.unitTest()
iTestCaseNumber = 0
if self.getListTest() == []:
self.__strReasonForNotBeingExecuted = "No test methods!"
else:
for pyTestMethod in self.getListTest():
iTestCaseNumber = iTestCaseNumber + 1
strMethodName = EDUtilsTest.patchMethodName(pyTestMethod)
EDVerbose.unitTest(
"-------------------------------------------------------------------"
)
EDVerbose.unitTest("Test case method : %s" % strMethodName)
EDVerbose.unitTest()
try:
pyTestMethod()
self.__iNumberTestMethodSuccess += 1
EDVerbose.unitTest("%s executed with SUCCESS" %
strMethodName)
EDVerbose.unitTest()
except AssertionError as pyException:
self.__dictMethodFailureMessages[strMethodName] = str(
pyException)
self.__iNumberTestMethodFailure += 1
EDVerbose.unitTest("Assertion Error Raised!")
EDVerbose.unitTest("%s executed with FAILURE" %
strMethodName)
EDVerbose.unitTest()
except Exception as pyException:
self.__dictMethodFailureMessages[strMethodName] = str(
pyException)
self.__iNumberTestMethodFailure += 1
EDVerbose.unitTest("Unexpected Error!")
EDVerbose.unitTest("%s executed with FAILURE" %
strMethodName)
EDVerbose.unitTest()
EDVerbose.writeErrorTrace()
EDVerbose.unitTest()
self.__bIsExecuted = True
self.setTimeEnd()
def postProcess(self):
"""
Writes out a summary of the test case.
"""
if self.__bIsExecuted:
EDVerbose.unitTest(
"-------------------------------------------------------------------"
)
EDVerbose.unitTest("Result for %s" % self.getClassName())
EDVerbose.unitTest()
EDVerbose.unitTest("Total number of test methods : %d" %
self.getNumberOfTests())
EDVerbose.unitTest("Number of SUCCESS : %d" %
self.__iNumberTestMethodSuccess)
EDVerbose.unitTest("Number of FAILURE : %d" %
self.__iNumberTestMethodFailure)
if self.__dictMethodFailureMessages != {}:
EDVerbose.unitTest("")
EDVerbose.unitTest("List of test methods ending with failure:")
for strMethodName in self.__dictMethodFailureMessages:
EDVerbose.unitTest(" %s :" % strMethodName.split(".")[1])
EDVerbose.unitTest(
" %s" %
self.__dictMethodFailureMessages[strMethodName])
EDVerbose.unitTest()
EDVerbose.unitTest("Runtime : %.3f [s]" %
self.getRunTime())
EDVerbose.unitTest(
"==================================================================="
)
else:
EDVerbose.unitTest()
EDVerbose.unitTest("Test case %s not executed :" %
self.getClassName())
EDVerbose.unitTest(self.__strReasonForNotBeingExecuted)
EDVerbose.unitTest()
EDVerbose.unitTest(
"==================================================================="
)
def postProcess(self):
"""
Writes out a summary of the test case.
"""
if self.__bIsExecuted:
EDVerbose.unitTest("-------------------------------------------------------------------")
EDVerbose.unitTest("Result for %s" % self.getClassName())
EDVerbose.unitTest()
EDVerbose.unitTest("Total number of test methods : %d" % self.getNumberOfTests())
EDVerbose.unitTest("Number of SUCCESS : %d" % self.__iNumberTestMethodSuccess)
EDVerbose.unitTest("Number of FAILURE : %d" % self.__iNumberTestMethodFailure)
if self.__dictMethodFailureMessages != {}:
EDVerbose.unitTest("")
EDVerbose.unitTest("List of test methods ending with failure:")
for strMethodName in self.__dictMethodFailureMessages:
EDVerbose.unitTest(" %s :" % strMethodName.split(".")[1])
EDVerbose.unitTest(" %s" % self.__dictMethodFailureMessages[strMethodName])
EDVerbose.unitTest()
EDVerbose.unitTest("Runtime : %.3f [s]" % self.getRunTime())
EDVerbose.unitTest("===================================================================")
else:
EDVerbose.unitTest()
EDVerbose.unitTest("Test case %s not executed :" % self.getClassName())
EDVerbose.unitTest(self.__strReasonForNotBeingExecuted)
EDVerbose.unitTest()
EDVerbose.unitTest("===================================================================")
def processKernel(self):
"""
Executes the test case.
"""
EDVerbose.DEBUG("EDTestCase.processKernel")
EDVerbose.screen()
EDVerbose.unitTest("===================================================================")
if self.getTestSuiteName() is not None:
EDVerbose.unitTest("TEST SUITE : %s" % self.getTestSuiteName())
EDVerbose.unitTest("TEST CASE : %s" % self.getClassName())
EDVerbose.unitTest(" ")
if self.__strReasonForNotBeingExecuted == "":
self.setTimeInit()
iNumberMethods = self.getNumberOfTests()
EDVerbose.unitTest("Total number of tests : %d" % iNumberMethods)
EDVerbose.unitTest()
iTestCaseNumber = 0
if self.getListTest() == []:
self.__strReasonForNotBeingExecuted = "No test methods!"
else:
for pyTestMethod in self.getListTest():
iTestCaseNumber = iTestCaseNumber + 1
strMethodName = EDUtilsTest.patchMethodName(pyTestMethod)
EDVerbose.unitTest("-------------------------------------------------------------------")
EDVerbose.unitTest("Test case method : %s" % strMethodName)
EDVerbose.unitTest()
try:
pyTestMethod()
self.__iNumberTestMethodSuccess += 1
EDVerbose.unitTest("%s executed with SUCCESS" % strMethodName)
EDVerbose.unitTest()
except AssertionError, pyException:
self.__dictMethodFailureMessages[strMethodName] = str(pyException)
self.__iNumberTestMethodFailure += 1
EDVerbose.unitTest("Assertion Error Raised!")
EDVerbose.unitTest("%s executed with FAILURE" % strMethodName)
EDVerbose.unitTest()
except Exception, pyException:
self.__dictMethodFailureMessages[strMethodName] = str(pyException)
self.__iNumberTestMethodFailure += 1
EDVerbose.unitTest("Unexpected Error!")
EDVerbose.unitTest("%s executed with FAILURE" % strMethodName)
EDVerbose.unitTest()
EDVerbose.writeErrorTrace()
EDVerbose.unitTest()
self.__bIsExecuted = True
self.setTimeEnd()
def postProcess(self):
"""
This method writes out the results of the test suite.
"""
EDVerbose.screen()
EDVerbose.screen()
EDVerbose.unitTest("###################################################################")
strResult = None
if self.__iNumberTestCaseFailure == 0 and self.__iNumberTestMethodFailure == 0:
strResult = "SUCCESS"
else:
strResult = "FAILURE"
EDVerbose.unitTest("Result for %s : %s" % (self.getTestName(), strResult))
EDVerbose.unitTest()
if self.__iNumberTestSuite > 0:
EDVerbose.unitTest(" Number of executed test suites in this test suite : %d" % self.__iNumberTestSuite)
EDVerbose.unitTest()
if self.__dictTestSuiteNotExecuted != {}:
EDVerbose.unitTest()
EDVerbose.unitTest("OBS! The following test suites were not executed due to errors:")
EDVerbose.unitTest()
for strTestSuiteName in self.__dictTestSuiteNotExecuted.keys():
EDVerbose.unitTest(" %s : %s" % (self.__dictTestSuiteNotExecuted[strTestSuiteName], strTestSuiteName))
EDVerbose.unitTest()
if self.__dictTestCaseNotExecuted != {}:
EDVerbose.unitTest()
EDVerbose.unitTest("OBS! The following test cases not executed due to errors:")
EDVerbose.unitTest()
for strTestCaseName in self.__dictTestCaseNotExecuted.keys():
EDVerbose.unitTest(" %s :" % strTestCaseName)
EDVerbose.unitTest(" %s" % self.__dictTestCaseNotExecuted[strTestCaseName])
EDVerbose.unitTest()
EDVerbose.unitTest(" Total number of test cases NOT EXECUTED : %d" % len(self.__dictTestCaseNotExecuted))
EDVerbose.unitTest()
if self.__iNumberTestCaseSuccess != 0 or self.__iNumberTestCaseFailure != 0:
EDVerbose.unitTest(" Total number of test cases executed with SUCCESS : %d" % self.__iNumberTestCaseSuccess)
EDVerbose.unitTest(" Total number of test cases executed with FAILURE : %d" % self.__iNumberTestCaseFailure)
EDVerbose.unitTest()
if self.__dictTestCaseFailureMessages != {}:
EDVerbose.unitTest("")
EDVerbose.unitTest("OBS! The following test methods ended with failure:")
EDVerbose.unitTest("")
for strTestCaseName in self.__dictTestCaseFailureMessages.keys():
EDVerbose.unitTest(" %s :" % strTestCaseName)
for strMethodName in self.__dictTestCaseFailureMessages[strTestCaseName].keys():
EDVerbose.unitTest(" %s :" % strMethodName.split(".")[1])
EDVerbose.unitTest(" %s" % self.__dictTestCaseFailureMessages[strTestCaseName][strMethodName])
EDVerbose.unitTest("")
EDVerbose.unitTest("")
if self.__iNumberTestMethodSuccess != 0 or self.__iNumberTestMethodFailure != 0:
EDVerbose.unitTest("Total number of test methods executed with SUCCESS : %d" % self.__iNumberTestMethodSuccess)
EDVerbose.unitTest("Total number of test methods executed with FAILURE : %d" % self.__iNumberTestMethodFailure)
EDVerbose.unitTest()
EDVerbose.unitTest(" Runtime : %.3f [s]" % self.getRunTime())
EDVerbose.unitTest("###################################################################")
