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")