def __init__(self, _edStringTestName=None):
EDTestCasePluginExecute.__init__(
self, 'EDPluginControlDIMPLEPrepareMTZFileForRefinementv10',
'EDPluginControlDIMPLEPrepareMTZFileForRefinement-v1.0',
_edStringTestName)
self.setConfigurationFile(
EDUtilsPath.mergePath(
self.getPluginTestsDataHome(),
'XSConfiguration_DIMPLEPrepareMTZFileForRefinement.xml'))
self.setDataInputFile(
EDUtilsPath.mergePath(
self.getPluginTestsDataHome(),
'XSDataInputDIMPLEPrepareMTZFileForRefinement_reference.xml'))
self.setReferenceDataOutputFile(
EDUtilsPath.mergePath(
self.getPluginTestsDataHome(),
'XSDataResultDIMPLEPrepareMTZFileForRefinement_reference.xml'))
self.m_edObtainedOutputDataFile = self.getPluginName() + '_output.xml'
self.m_iNoErrorMessages = 0
self.m_iNoWarningMessages = 0
def preProcess(self, _edObject=None):
"""
"""
EDPluginExecProcessScript.preProcess(self)
self.setFileBestDat(EDUtilsPath.mergePath(self.getWorkingDirectory(), "bestfile.dat"))
self.setFileBestPar(EDUtilsPath.mergePath(self.getWorkingDirectory(), "bestfile.par"))
EDUtilsFile.writeFile(self.getFileBestDat(), self.getDataInput().getBestFileContentDat().getValue())
EDUtilsFile.writeFile(self.getFileBestPar(), self.getDataInput().getBestFileContentPar().getValue())
listBestFileContentHKL = self.getDataInput().getBestFileContentHKL()
iterator = 0
for bestFileContentHKL in listBestFileContentHKL:
iterator = iterator + 1
bestFileHKL = os.path.join(self.getWorkingDirectory(), "bestfile" + str(iterator) + ".hkl")
self.listFileBestHKL.append(bestFileHKL)
EDUtilsFile.writeFile(bestFileHKL, bestFileContentHKL.getValue())
if(self.getDataInput().getComplexity() is not None):
self.setComplexity(self.getDataInput().getComplexity().getValue())
self.initializeCommands()
def __init__(self, _pyStrTestName=None):
EDTestCase.__init__(self, _pyStrTestName)
strKernelDataHome = EDUtilsTest.getPluginTestDataDirectory(self.getClassName())
strDataDir = "EDHandlerRaddosev10"
self.strDataPath = EDUtilsPath.mergePath(strKernelDataHome, strDataDir)
self.strReferenceInputFile2 = EDUtilsPath.mergePath(self.strDataPath, "XSDataRaddosev10Input_reference_02.xml")
self.strObtainedInputFile2 = "XSDataInputRaddosev10FromObject_02.xml"
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath,
strReferenceInputControlISPyBFile)
strXMLIndexingInput = self.readAndParseFile(strPath)
from XSDataMXv1 import XSDataInputControlISPyB
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(
strXMLIndexingInput)
from EDHandlerXSDataISPyBv1_1 import EDHandlerXSDataISPyBv1_1
xsDataInputISPyB = EDHandlerXSDataISPyBv1_1.generateXSDataInputISPyB(
xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath,
strReferenceInputISPyBFile)
strXMLInputISPyBReference = self.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataInputISPyB
xsDataInputISPyBReference = XSDataInputISPyB.parseString(
strXMLInputISPyBReference)
# Remove the time strings since they otherwise make the test fail
xsDataInputISPyBReference.getScreening().setTimeStamp(None)
xsDataInputISPyB.getScreening().setTimeStamp(None)
EDAssert.equal(xsDataInputISPyBReference.marshal(),
xsDataInputISPyB.marshal())
def __init__(self, _oalStringTestName=None):
"""
"""
EDTestCasePluginExecuteBestv1_2.__init__(self, "EDPluginBestv1_2")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataInputBest_withDamPar.xml"))
self.setReferenceDataOutputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataResultBest_withDamPar.xml"))
def testSetDataModelInput(self):
edPluginBest = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(EDUtilsPath.mergePath(self.m_pyStrDataPath, "XSConfiguration.xml"))
edPluginBest.setConfiguration(xsPluginItemGood01)
edPluginBest.setScriptExecutable("cat")
edPluginBest.configure()
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBest = XSDataInputBest()
from XSDataCommon import XSDataAbsorbedDoseRate
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataTime
from XSDataCommon import XSDataFile
from XSDataCommon import XSDataSpeed
from XSDataCommon import XSDataString
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataBoolean
xsDataInputBest.setCrystalAbsorbedDoseRate(XSDataAbsorbedDoseRate(0.22E+06))
xsDataInputBest.setCrystalShape(XSDataDouble(1))
xsDataInputBest.setCrystalSusceptibility(XSDataDouble(1.5))
xsDataInputBest.setDetectorType(XSDataString("q210-2x"))
xsDataInputBest.setBeamExposureTime(XSDataTime(1))
xsDataInputBest.setBeamMaxExposureTime(XSDataTime(10000))
xsDataInputBest.setBeamMinExposureTime(XSDataTime(0.1))
xsDataInputBest.setGoniostatMinRotationWidth(XSDataAngle(0.1))
xsDataInputBest.setGoniostatMaxRotationSpeed(XSDataSpeed(10))
xsDataInputBest.setAimedResolution(XSDataDouble(2))
xsDataInputBest.setAimedRedundancy(XSDataDouble(6.5))
xsDataInputBest.setAimedCompleteness(XSDataDouble(0.9))
xsDataInputBest.setAimedIOverSigma(XSDataDouble(3))
xsDataInputBest.setComplexity(XSDataString("min"))
xsDataInputBest.setAnomalousData(XSDataBoolean(False))
fileDirectory = edPluginBest.getWorkingDirectory()
bestFileContentDat = EDUtilsFile.readFile(EDUtilsPath.mergePath(self.m_pyStrDataPath, "bestfile.dat"))
xsDataInputBest.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(EDUtilsPath.mergePath(self.m_pyStrDataPath, "bestfile.par"))
xsDataInputBest.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(EDUtilsPath.mergePath(self.m_pyStrDataPath, "bestfile1.hkl"))
xsDataInputBest.addBestFileContentHKL(XSDataString(bestFileContentHKL))
xsDataInputBest.outputFile(self.m_edObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile (self.m_edReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile (self.m_edObtainedInputFile)
xsDataInputExpected = XSDataInputBest.parseString(pyStrExpectedInput)
xsDataInputObtained = XSDataInputBest.parseString(pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
EDUtilsFile.deleteFile(self.m_edObtainedInputFile)
self.cleanUp(edPluginBest)
def __init__(self, _pyStrTestName=None):
EDTestCasePluginUnit.__init__(self, "EDPluginBestv1_2")
self.m_pyStrDataPath = self.getPluginTestsDataHome()
self.m_edObtainedInputFile = "XSDataInputBest_test.xml"
self.m_edReferenceInputFile = EDUtilsPath.mergePath(self.m_pyStrDataPath, "XSDataInputBest_reference.xml")
self.m_edReferenceResultFile = EDUtilsPath.mergePath(self.m_pyStrDataPath, "XSDataResultBest_reference.xml")
self.m_edReferenceScriptLogFileName = EDUtilsPath.mergePath(self.m_pyStrDataPath, "EDPluginBestv1_2.log")
def __init__(self, _oalStringTestName=None):
EDTestCasePluginExecuteBestv1_2.__init__(self, "EDPluginBestv1_2")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataInputBest_withMinTransmissionInput.xml"))
if (self.m_bRunOnIntel):
self.setReferenceDataOutputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataResultBest_withTransmissionInputForIntel.xml"))
else:
self.setReferenceDataOutputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataResultBest_withTransmissionInput.xml"))
def __init__(self, _pyStrTestName=None):
EDTestCase.__init__(self, _pyStrTestName)
strKernelDataHome = EDUtilsTest.getPluginTestDataDirectory(
self.getClassName())
strDataDir = "EDHandlerRaddosev10"
self.strDataPath = EDUtilsPath.mergePath(strKernelDataHome, strDataDir)
self.strReferenceInputFile2 = EDUtilsPath.mergePath(
self.strDataPath, "XSDataRaddosev10Input_reference_02.xml")
self.strObtainedInputFile2 = "XSDataInputRaddosev10FromObject_02.xml"
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataInputISPyB = EDHandlerXSDataISPyBv1_4.generateXSDataInputISPyBStoreScreening(xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = EDUtilsFile.readFileAndParseVariables(strReferencePath, self.dictReplace)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_4")
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataInputISPyB = EDHandlerXSDataISPyBv1_3.generateXSDataInputISPyBStoreScreening(xsDataInputControlISPyB)
print xsDataInputISPyB.marshal()
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = EDUtilsFile.readFileAndParseVariables(strReferencePath, self.dictReplace)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_3")
def __init__(self, _strTestName=None):
EDTestCase.__init__(self, "EDTestCaseEDConfiguration")
strKernelDataHome = EDUtilsTest.getPluginTestDataDirectory(
self.getClassName())
strDataDir = "EDConfiguration"
self.strDataPath = EDUtilsPath.mergePath(strKernelDataHome, strDataDir)
self.strEdnaSiteOrig = EDUtilsPath.getEdnaSite()
def __init__(self, _edStringTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginSTACAlignmentv2_0")
edStringPluginTestDataHome = self.getPluginTestsDataHome()
self.m_edStringExecutionTestDataInputHome = EDUtilsPath.mergePath(edStringPluginTestDataHome, "executionTestInput")
self.m_edStringExecutionTestDataResultHome = EDUtilsPath.mergePath(edStringPluginTestDataHome, "executionTestResult")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(os.path.join(self.m_edStringExecutionTestDataInputHome, "EDPluginSTACAlignmentv2_0_dataInputBest_reference.xml"), "inputBest")
self.setDataInputFile(os.path.join(self.m_edStringExecutionTestDataInputHome, "EDPluginSTACAlignmentv2_0_dataInputDataCollection_reference.xml"), "dataCollection")
self.setDataInputFile(os.path.join(self.m_edStringExecutionTestDataInputHome, "EDPluginSTACAlignmentv2_0_dataInputIndexingResult_reference.xml"), "indexingResult")
self.__pyStrBCMDEFReference = os.path.join(self.m_edStringExecutionTestDataInputHome, "BCM.dat")
self.setReferenceDataOutputFile(os.path.join(self.m_edStringExecutionTestDataResultHome, "EDPluginSTACAlignmentv2_0_dataOutput_reference.xml"))
#self.m_edObtainedOutputDataFile = self.getPluginName() + "_dataOutput.xml"
self.m_edObtainedOutputDataFile = self.getPluginName() + "_output.xml"
self.setNoExpectedWarningMessages(1)
def testGetBestWilsonPlotPath(self):
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataCharacterisationResult = xsDataInputControlISPyB.characterisationResult
strPath = EDHandlerXSDataISPyBv1_4.getBestWilsonPlotPath(xsDataCharacterisationResult)
EDAssert.equal(True, strPath.endswith("B.jpg"), "Wilson plot path extracted from characterisation results")
def __init__( self, _edStringTestName = None):
"""
"""
EDTestCasePluginExecute.__init__( self, "EDPluginExecDIMPLEMTZDUMPv10" )
self.setConfigurationFile( self.getRefConfigFile() )
self.setDataInputFile( EDUtilsPath.mergePath( self.getPluginTestsDataHome(), \
"XSDataInputDIMPLEMTZDUMP_reference.xml" ) )
self.setReferenceDataOutputFile( EDUtilsPath.mergePath( self.getPluginTestsDataHome(), \
"XSDataResultDIMPLEMTZDUMP_reference.xml"))
self.m_edObtainedOutputDataFile = self.getPluginName() + "_output.xml"
self.m_iNoErrorMessages = 0
self.m_iNoWarningMessages = 0
def __init__(self, _edStringTestName = None):
EDTestCasePluginExecute.__init__(self, 'EDPluginExecDIMPLEREINDEXv10')
self.setConfigurationFile( self.getRefConfigFile() )
self.setDataInputFile(EDUtilsPath.mergePath(
self.getPluginTestsDataHome(),
'XSDataInputDIMPLEREINDEX_reference.xml'))
self.setReferenceDataOutputFile(EDUtilsPath.mergePath(
self.getPluginTestsDataHome(),
'XSDataResultDIMPLEREINDEX_reference.xml'))
self.m_edObtainedOutputDataFile = '%s_output.xml' % \
self.getPluginName()
self.m_iNoErrorMessages = 0
self.m_iNoWarningMessages = 0
def __init__( self, _edStringTestName = None):
"""
"""
EDTestCasePluginExecute.__init__( self, "EDPluginControlTomographyv10", "EDPluginControlTomography-v1.0", _edStringTestName )
self.setConfigurationFile( EDUtilsPath.mergePath( self.getPluginTestsDataHome(),
"XSConfiguration_Tomography.xml" ) )
self.setDataInputFile( EDUtilsPath.mergePath( self.getPluginTestsDataHome(), \
"XSDataInputTomography_reference.xml" ) )
self.setReferenceDataOutputFile( EDUtilsPath.mergePath( self.getPluginTestsDataHome(), \
"XSDataResultTomography_reference.xml"))
self.m_edObtainedOutputDataFile = self.getPluginName() + "_output.xml"
self.m_iNoErrorMessages = 0
self.m_iNoWarningMessages = 0
def __init__(self, _edStringTestName=None):
EDTestCasePluginExecute.__init__(self,
'EDPluginExecDIMPLETRUNCATETESTv10')
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(
EDUtilsPath.mergePath(self.getPluginTestsDataHome(),
'XSDataInputDIMPLETRUNCATE_reference.xml'))
self.setReferenceDataOutputFile(
EDUtilsPath.mergePath(self.getPluginTestsDataHome(),
'XSDataResultDIMPLETRUNCATE_reference.xml'))
self.m_edObtainedOutputDataFile = '%s_output.xml' % \
self.getPluginName()
self.m_iNoErrorMessages = 0
self.m_iNoWarningMessages = 0
def __init__(self, _edStringTestName=None):
EDTestCasePluginUnit.__init__(self, "EDPluginMOSFLMIndexingv10")
strDataImageDir = "images"
self.strDataImagePath = os.path.join(self.getTestsDataHome(), strDataImageDir)
strPluginTestDataHome = self.getPluginTestsDataHome()
self.strUnitTestDataHome = EDUtilsPath.mergePath(strPluginTestDataHome, "unitTest")
self.strReferenceDataInputFile = os.path.join(self.strUnitTestDataHome, "XSDataMOSFLMInputIndexing_reference.xml")
self.strReferenceDataOutputFile = os.path.join(self.strUnitTestDataHome, "XSDataMOSFLMOutputIndexing_reference.xml")
def __init__(self, _edStringTestName = None):
EDTestCasePluginExecute.__init__(
self, 'EDPluginControlDIMPLEPipelineCalcDiffMapv10',
'EDPluginControlDIMPLEPipelineCalcDiffMap-v1.0', _edStringTestName)
self.setConfigurationFile(EDUtilsPath.mergePath(
self.getPluginTestsDataHome(),
'XSConfiguration_DIMPLEPipelineCalcDiffMap.xml'))
self.setDataInputFile(EDUtilsPath.mergePath(
self.getPluginTestsDataHome(),
'XSDataInputDIMPLEPipelineCalcDiffMap_reference.xml'))
self.setReferenceDataOutputFile(EDUtilsPath.mergePath(
self.getPluginTestsDataHome(),
'XSDataResultDIMPLEPipelineCalcDiffMap_reference.xml'))
self.m_edObtainedOutputDataFile = self.getPluginName() + '_output.xml'
self.m_iNoErrorMessages = 0
self.m_iNoWarningMessages = 0
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = self.readAndParseFile(strPath)
from XSDataMXv1 import XSDataInputControlISPyB
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
from EDHandlerXSDataISPyBv1_1 import EDHandlerXSDataISPyBv1_1
xsDataInputISPyB = EDHandlerXSDataISPyBv1_1.generateXSDataInputISPyB(xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = self.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataInputISPyB
xsDataInputISPyBReference = XSDataInputISPyB.parseString(strXMLInputISPyBReference)
# Remove the time strings since they otherwise make the test fail
xsDataInputISPyBReference.getScreening().setTimeStamp(None)
xsDataInputISPyB.getScreening().setTimeStamp(None)
EDAssert.equal(xsDataInputISPyBReference.marshal(), xsDataInputISPyB.marshal())
def __init__(self, _edStringTestName=None):
"""
"""
EDTestCasePluginExecute.__init__(self, "EDPluginControlTomographyv10",
"EDPluginControlTomography-v1.0",
_edStringTestName)
self.setConfigurationFile(
EDUtilsPath.mergePath(self.getPluginTestsDataHome(),
"XSConfiguration_Tomography.xml"))
self.setDataInputFile( EDUtilsPath.mergePath( self.getPluginTestsDataHome(), \
"XSDataInputTomography_reference.xml" ) )
self.setReferenceDataOutputFile( EDUtilsPath.mergePath( self.getPluginTestsDataHome(), \
"XSDataResultTomography_reference.xml"))
self.m_edObtainedOutputDataFile = self.getPluginName() + "_output.xml"
self.m_iNoErrorMessages = 0
self.m_iNoWarningMessages = 0
def __init__(self, _oalStringTestName=None):
EDTestCasePluginExecute.__init__(self, "EDPluginBestv1_2")
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataInputBest_reference.xml"))
#
# If on Linux, check if run on Intel processor
#
self.m_bRunOnIntel = False
pyStrSystem = os.uname()[0]
if (pyStrSystem == "Linux"):
pyFile = open("/proc/cpuinfo", "r")
pyListCpuInfo = pyFile.readlines()
pyFile.close()
for pyStrLine in pyListCpuInfo:
if (pyStrLine.find("vendor_id") != -1):
if (pyStrLine.find("GenuineIntel") != -1):
self.m_bRunOnIntel = True
if (self.m_bRunOnIntel):
self.setReferenceDataOutputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataResultBest_referenceForIntel.xml"))
else:
self.setReferenceDataOutputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataResultBest_reference.xml"))
def __init__(self, _strTestName=None):
"""
"""
EDTestCasePluginUnit.__init__(self, "EDPluginMOSFLMIntegrationv10", "EDPluginGroupMOSFLM-v1.0", _strTestName)
strPluginTestDataHome = self.getPluginTestsDataHome()
self.strUnitTestDataHome = EDUtilsPath.mergePath(strPluginTestDataHome, "unitTest")
self.strReferenceDataInputFile = os.path.join(self.strUnitTestDataHome, "XSDataMOSFLMInputIntegration_reference.xml")
self.strReferenceDataOutputFile = os.path.join(self.strUnitTestDataHome, "XSDataMOSFLMOutputIntegration_reference.xml")
strDataImageDir = "images"
self.strDataImagePath = os.path.join(self.getTestsDataHome(), strDataImageDir)
def testConfigureOK(self):
edPluginBest = self.createPlugin()
strConfigPath = EDUtilsPath.mergePath(self.strDataPath, "XSConfiguration.xml")
xsPluginItemGood01 = self.getPluginConfiguration(strConfigPath)
edPluginBest.setConfiguration(xsPluginItemGood01)
edPluginBest.setScriptExecutable("cat")
edPluginBest.configure()
EDAssert.equal("/bin/bash", edPluginBest.getScriptShell())
EDAssert.equal("cat", edPluginBest.getScriptExecutable())
EDAssert.equal("/opt/pxsoft/ccp4-6.0.2/include/ccp4.setup-bash.orig", edPluginBest.getSetupCCP4())
EDAssert.equal("Version of Best to be tested", edPluginBest.getStringVersion())
# EDAssert.equal(600, edPluginMessage.getTimeOut())
EDAssert.equal("/home/sweet/home", edPluginBest.getBestHome())
EDAssert.equal("export besthome=/home/sweet/home", edPluginBest.getCommandBestHome())
self.cleanUp(edPluginBest)
def testGetBestWilsonPlotPath(self):
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath,
strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(
strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(
strXMLIndexingInput)
xsDataCharacterisationResult = xsDataInputControlISPyB.characterisationResult
strPath = EDHandlerXSDataISPyBv1_4.getBestWilsonPlotPath(
xsDataCharacterisationResult)
EDAssert.equal(
True, strPath.endswith("B.jpg"),
"Wilson plot path extracted from characterisation results")
def finallyProcess(self, _edObject=None):
EDPluginExecProcessScript.finallyProcess(self)
EDVerbose.DEBUG("EDPluginBestv1_2.finallyProcess")
strError = self.readProcessErrorLogFile()
if((strError is not None) and (strError != "")):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginBestv1_2.postProcess', 'EDPluginBestv1_2', strError)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setDataOutput(XSDataResultBest())
self.setFailure()
else:
xsDataResultBest = self.getOutputDataFromDNATableFile(EDUtilsPath.mergePath(self.getWorkingDirectory(), self.getScriptBaseName() + "_dnaTables.xml"))
xsDataFilePathToLog = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName())))
xsDataResultBest.setPathToLogFile(xsDataFilePathToLog)
self.setDataOutput(xsDataResultBest)
def testSetDataInput(self):
"""
"""
edPluginXDSIndexingv1_0 = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "EDPluginXDSIndexingv1_0_configuration_OK_01.xml"))
edPluginXDSIndexingv1_0.setConfiguration(xsPluginItemGood01)
edPluginXDSIndexingv1_0.setScriptExecutable("cat")
edPluginXDSIndexingv1_0.configure()
from XSDataXDSv1_0 import XSDataInputXDSIndexing
xmlInput = self.readAndParseFile(self.strReferenceInputFile)
xsDataXDSIndexingInputReference = XSDataInputXDSIndexing.parseString(xmlInput)
xsDataXDSIndexingInputReference.outputFile("XSDataInputXDSIndexing_reference.xml")
edPluginXDSIndexingv1_0.setDataInput(xmlInput)
xsDataXDSIndexingInput = edPluginXDSIndexingv1_0.getDataInput()
xsDataXDSIndexingInput.outputFile("XSDataInputXDSIndexing.xml")
EDAssert.equal(xsDataXDSIndexingInputReference.marshal(), xsDataXDSIndexingInput.marshal())
self.cleanUp(edPluginXDSIndexingv1_0)
def __init__(self, _strTestName=None):
EDTestCase.__init__(self, "EDTestCaseEDConfiguration")
strKernelDataHome = EDUtilsTest.getPluginTestDataDirectory(self.getClassName())
strDataDir = "EDConfiguration"
self.strDataPath = EDUtilsPath.mergePath(strKernelDataHome, strDataDir)
self.strEdnaSiteOrig = EDUtilsPath.getEdnaSite()
def __init__(self, _strTestName=None):
EDTestCasePluginUnit.__init__(self, "EDPluginSTACv2_0")
strPluginTestDataHome = self.getPluginTestsDataHome()
self.strUnitTestDataHome = EDUtilsPath.mergePath(strPluginTestDataHome, "unitTest")
def __init__(self, _pyStrTestName="EDPluginXDSGenerateBackgroundImagev1_0"):
EDTestCasePluginExecute.__init__(self, _pyStrTestName)
self.setConfigurationFile(self.getRefConfigFile())
self.setDataInputFile(EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataInputXDSIndexing_reference.xml"))
def __init__(self, _pyStrTestName="EDPluginXDSSpotSearchv1_1"):
"""
Set up paths, reference files etc.
"""
EDTestCasePluginUnit.__init__(self, _pyStrTestName)
self.m_pyStrReferenceInputFile = EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataInputXDSSpotSearch_reference.xml")
def initializeCommands(self):
self.addListCommandPreExecution(self.__strCommandBestHome)
listFileBestHKL = self.getListFileBestHKL()
listFileBestHKLCommand = ""
for fileBestHKL in listFileBestHKL:
listFileBestHKLCommand = listFileBestHKLCommand + fileBestHKL + " "
strDetectorName = self.getDataInput().getDetectorType().getValue()
fExposureTime = self.getDataInput().getBeamExposureTime().getValue()
fMaxExposureTime = self.getDataInput().getBeamMaxExposureTime().getValue()
self.__strCommandBest = "-f " + strDetectorName + " " + "-t " + str(fExposureTime) + " "
if(self.getDataInput().getBeamMinExposureTime() is not None):
strBeamMinExposureTime = str(self.getDataInput().getBeamMinExposureTime().getValue())
self.__strCommandBest = self.__strCommandBest + "-M " + strBeamMinExposureTime + " "
if(self.getDataInput().getGoniostatMaxRotationSpeed() is not None):
strGoniostatMaxRotationSpeed = str(self.getDataInput().getGoniostatMaxRotationSpeed().getValue())
self.__strCommandBest = self.__strCommandBest + "-S " + strGoniostatMaxRotationSpeed + " "
if(self.getDataInput().getGoniostatMinRotationWidth() is not None):
strGoniostatMinRotationWidth = str(self.getDataInput().getGoniostatMinRotationWidth().getValue())
self.__strCommandBest = self.__strCommandBest + "-w " + strGoniostatMinRotationWidth + " "
if(self.getDataInput().getAimedResolution() is not None):
strAimedResolution = str(self.getDataInput().getAimedResolution().getValue())
self.__strCommandBest = self.__strCommandBest + "-r " + strAimedResolution + " "
if(self.getDataInput().getAimedRedundancy() is not None):
strAimedRedundancy = str(self.getDataInput().getAimedRedundancy().getValue())
self.__strCommandBest = self.__strCommandBest + "-R " + strAimedRedundancy + " "
if(self.getDataInput().getAimedCompleteness() is not None):
strAimedCompleteness = str(self.getDataInput().getAimedCompleteness().getValue())
self.__strCommandBest = self.__strCommandBest + "-C " + strAimedCompleteness + " "
if(self.getDataInput().getAimedIOverSigma() is not None):
strAimedIOverSigma = str(self.getDataInput().getAimedIOverSigma().getValue())
self.__strCommandBest = self.__strCommandBest + "-i2s " + strAimedIOverSigma + " "
if(self.getDataInput().getCrystalAbsorbedDoseRate() is not None):
strCrystalAbsorbedDoseRate = str(self.getDataInput().getCrystalAbsorbedDoseRate().getValue())
self.__strCommandBest = self.__strCommandBest + "-GpS " + strCrystalAbsorbedDoseRate + " "
if(self.getDataInput().getCrystalShape() is not None):
strCrystalShape = str(self.getDataInput().getCrystalShape().getValue())
self.__strCommandBest = self.__strCommandBest + "-sh " + strCrystalShape + " "
if(self.getDataInput().getCrystalSusceptibility() is not None):
strCrystalSusceptibility = str(self.getDataInput().getCrystalSusceptibility().getValue())
self.__strCommandBest = self.__strCommandBest + "-su " + strCrystalSusceptibility + " "
if(self.getDataInput().getTransmission() is not None):
strTransmission = str(self.getDataInput().getTransmission().getValue())
self.__strCommandBest = self.__strCommandBest + "-Trans " + strTransmission + " "
if(self.getDataInput().getMinTransmission() is not None):
strMinTransmission = str(self.getDataInput().getMinTransmission().getValue())
self.__strCommandBest = self.__strCommandBest + "-TRmin " + strMinTransmission + " "
if(self.getDataInput().getNumberOfCrystalPositions() is not None):
iNumberOfCrystalPositions = str(self.getDataInput().getNumberOfCrystalPositions().getValue())
self.__strCommandBest = self.__strCommandBest + "-Npos " + iNumberOfCrystalPositions + " "
if(self.getDataInput().getDetectorDistanceMin() is not None):
fDetectorDistanceMin = str(self.getDataInput().getDetectorDistanceMin().getValue())
self.__strCommandBest = self.__strCommandBest + "-DIS_MIN " + fDetectorDistanceMin + " "
if(self.getDataInput().getDetectorDistanceMax() is not None):
fDetectorDistanceMax = str(self.getDataInput().getDetectorDistanceMax().getValue())
self.__strCommandBest = self.__strCommandBest + "-DIS_MAX " + fDetectorDistanceMax + " "
if(self.getDataInput().getAnomalousData() is not None):
bAnomalousData = self.getDataInput().getAnomalousData().getValue()
if (bAnomalousData):
if(self.getDataInput().getCrystalAbsorbedDoseRate() is not None):
self.__strCommandBest = self.__strCommandBest + "-asad "
else:
self.__strCommandBest = self.__strCommandBest + "-a "
strStrategyOption = self.getDataInput().getStrategyOption()
if(strStrategyOption is not None):
self.__strCommandBest = self.__strCommandBest + "%s " % strStrategyOption.getValue()
self.__strCommandBest = self.__strCommandBest + "-T " + str(fMaxExposureTime) + " " + \
"-dna " + self.getScriptBaseName() + "_dnaTables.xml" + " " + \
"-o " + EDUtilsPath.mergePath(self.getWorkingDirectory(), self.getScriptBaseName() + "_plots.mtv ") + \
"-e " + self.getComplexity() + " "
if self.getDataInput().getXdsBackgroundImage():
strPathToXdsBackgroundImage = self.getDataInput().getXdsBackgroundImage().getPath().getValue()
self.__strCommandBest = self.__strCommandBest + "-MXDS " + self.getFileBestPar() + " " + strPathToXdsBackgroundImage + " " + listFileBestHKLCommand
else:
self.__strCommandBest = self.__strCommandBest + "-mos " + self.getFileBestDat() + " " + self.getFileBestPar() + " " + listFileBestHKLCommand
self.setScriptCommandline(self.__strCommandBest)
def __init__(self, _strTestName="EDPluginXDSv1_0"):
EDTestCasePluginUnit.__init__(self, _strTestName)
self.m_strReferenceDataInputFile = EDUtilsPath.mergePath(self.getPluginTestsDataHome(), "XSDataInputXDSIndexing_reference.xml")
