def test_generateCommandLine(self):
edPlugin = self.getPlugin()
strInputXML = EDUtilsFile.readFile(os.path.join(self.strDataPath, "XSDataInputAutoPROC_reference.xml"))
xsDataInput = XSDataInputAutoPROC.parseString(strInputXML)
strCommandLine = edPlugin.generateCommandLine(xsDataInput)
print(strCommandLine)
EDAssert.equal("-B -xml -I /scisoft/pxsoft/data/AUTO_PROCESSING/id29/20130301/RAW_DATA/GaelleB/xtal5 -Id 1088454,/scisoft/pxsoft/data/AUTO_PROCESSING/id29/20130301/RAW_DATA/GaelleB/xtal5,xtal5w1_1_####.cbf,1,100 -R 5.0 2.0 -ANO", strCommandLine, "Reference data input")
def testGenerateMosflmScriptName(self):
"""
This method tests the generateMosflmScriptName method of the Labelit plugin.
"""
edPluginLabelitv10 = self.createPlugin()
EDAssert.equal("integration01.csh", edPluginLabelitv10.generateMosflmScriptName(1))
EDAssert.equal("integration10.csh", edPluginLabelitv10.generateMosflmScriptName(10))
def testGetOutputDataFromDNATableFile(self):
edPluginRdfit = self.createPlugin()
strPathToTableFile = os.path.join(self.strDataPath, "rdfit.xml")
xsDataResultRdfit = edPluginRdfit.getOutputDataFromDNATableFile(strPathToTableFile)
strPathToReference = os.path.join(self.strDataPath, "XSDataResultRdfit_reference.xml")
xsDataResultRdfitReference = XSDataResultRdfit.parseFile(strPathToReference)
EDAssert.equal(xsDataResultRdfitReference.marshal(), xsDataResultRdfit.marshal(), "Test parsing result 'DNA' xml file")
def testExecute(self):
EDTestCasePluginExecuteControlCharacterisationv1_4.testExecute(self)
edPlugin = self.getPlugin()
strStatusMessage = None
if edPlugin.hasDataOutput("statusMessage"):
strStatusMessage = edPlugin.getDataOutput(
"statusMessage")[0].getValue()
EDAssert.equal(
True,
strStatusMessage.find("Strategy calculation FAILURE") != -1,
"Status message contains 'Strategy calculation FAILURE'")
def testExecute(self):
self.run()
plugin = self.getPlugin()
EDVerbose.DEBUG('Checking error messages...')
EDAssert.equal(self.m_iNoErrorMessages,
self.getErrorMessages().getNumberObjects())
EDVerbose.DEBUG('Checking warning messages...')
EDAssert.equal(self.m_iNoWarningMessages,
self.getWarningMessages().getNumberObjects())
def unitTestSetGetData(self):
"""
check the status after a job creation
"""
EDVerbose.DEBUG("EDTestCaseEDJob.unitTestSetGetData")
edJob = EDJob(self.strPluginName)
edJob.setDataInput(self.strXmlInput)
EDAssert.equal(self.strXmlInput,
edJob.getDataInput().strip(),
"Data Input is correctly set")
EDAssert.equal("uninitialized", edJob.getStatus(),
"Job %s is still ''uninitialized''" % edJob.getJobId())
def testCreatePyarchHtmlDirectoryPath(self):
strTestDataDir = self.getPluginTestsDataHome()
strTestFile = os.path.join(strTestDataDir, "EDHandlerESRFPyarchv1_0",
"XSDataCollection_reference.xml")
strXml = self.readAndParseFile(strTestFile)
xsDataCollection = XSDataCollection.parseString(strXml)
strPyarchHtmlDirectoryPath = EDHandlerESRFPyarchv1_0.createPyarchHtmlDirectoryPath(
xsDataCollection)
# print strPyarchHtmlDirectoryPath
strReferencePath = "/data/pyarch/2016/id30b/opid30b/20161214/RAW_DATA/Magda/Test_x1_2_dnafiles"
EDAssert.equal(strReferencePath, strPyarchHtmlDirectoryPath,
"Correct pyarch path")
def preProcess(self, _edObject=None):
EDPluginExec.preProcess(self)
self.DEBUG("EDPluginExecMeasureOffsetv1_0.preProcess")
sdi = self.dataInput
images = sdi.image
arrays = sdi.array
if len(images) == 2:
self.npaIm1 = numpy.array(EDUtilsArray.getArray(images[0]))
self.npaIm2 = numpy.array(EDUtilsArray.getArray(images[1]))
elif len(arrays) == 2:
self.npaIm1 = EDUtilsArray.xsDataToArray(arrays[0])
self.npaIm2 = EDUtilsArray.xsDataToArray(arrays[1])
else:
strError = "EDPluginExecMeasureOffsetv1_0.preProcess: You should either provide two images or two arrays, but I got: %s" % sdi.marshal(
)[:1000]
self.ERROR(strError)
self.setFailure()
raise RuntimeError(strError)
crop = sdi.cropBorders
if len(crop) > 1:
self.tCrop = tuple([i.value for i in crop])
elif len(crop) == 1:
self.tCrop = (crop[0].value, crop[0].value)
center = sdi.center
if len(center) > 1:
self.tCenter = tuple([i.value for i in center])
elif len(center) == 1:
self.tCenter = (center[0].value, center[0].value)
width = sdi.width
if len(width) > 1:
self.tWidth = tuple([i.value for i in width])
elif len(width) == 1:
self.tWidth = (width[0].value, width[0].value)
smooth = sdi.smoothBorders
if len(smooth) == 2:
self.tSmooth = (smooth[0].value, smooth[1].value)
elif len(smooth) == 1:
self.tSmooth = (smooth[0].value, smooth[0].value)
if sdi.backgroundSubtraction is not None:
self.bBackgroundsubtraction = (sdi.backgroundSubtraction.value
in [1, True, "true"])
if sdi.sobelFilter is not None:
self.sobel = (sdi.sobelFilter in [1, True, "true"])
EDAssert.equal(self.npaIm1.shape, self.npaIm2.shape,
"Images have the same size")
def testPopulateXSDataInputSPDCake(self):
edPluginControlID11 = self.createPlugin()
xsDataInputSPDCake = edPluginControlID11.populateXSDataInputSPDCake(
self.dictID11Reference)
strDataPath = self.getPluginTestsDataHome()
strReferenceFile = "XSDataInputSPDCake_fromDict.xml"
strPath = os.path.join(strDataPath, strReferenceFile)
xsDataInputSPDCakeReference = XSDataInputSPDCake.parseString(
self.readAndParseFile(strPath))
xsDataInputSPDCakeReference.setDeleteCorImg(
XSDataBoolean(not (EDVerbose.isVerboseDebug())))
EDAssert.equal(xsDataInputSPDCakeReference.marshal(),
xsDataInputSPDCake.marshal())
def unitTestXsdToArray(self):
"""
test the execution of xsDataToArray static method
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsArray.unitTestXsdToArray")
if numpy is not None:
EDAssert.arraySimilar(self.arrayNumpy,
EDUtilsArray.xsDataToArray(self.xsDataArrayNumpy, _bForceNoNumpy=False),
_strComment="Array are the same (Numpy used)")
else:
EDAssert.equal(self.arrayNoNumpy,
EDUtilsArray.xsDataToArray(self.xsDataArrayNumpy, _bCheckMd5sum=True, _bForceNoNumpy=False),
"Array are the same (no Numpy available)")
def testStaticEDConfiguration(self):
# This test make sure that changing an instatiation of EDConfiguration does not change the
# corresponding plugin configuration for EDConfigurationStatic
strPathToTestConfigFile = os.path.join(
self.strDataPath, "XSConfiguration_testNonStatic.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
strParam1 = edConfiguration.getStringValue("EDPluginTestPluginFactory",
"testItemName")
EDUtilsPath.setEdnaSite("TestStaticConfiguration")
strParam2 = EDConfigurationStatic.getStringValue(
"EDPluginTestPluginFactory", "testItemName")
EDAssert.equal(False, strParam1 == strParam2,
"Static config is not equal to local config")
def unitTestArchSize(self):
"""
Test architecture and size
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsPlatform.unitTestArchSize")
if EDUtilsPlatform.size == 64:
EDAssert.equal(distutils.util.get_platform(),
EDUtilsPlatform.getPythonPlatform(),
"distutil.util.get_platform")
else:
EDAssert.equal(distutils.util.get_platform(),
EDUtilsPlatform.getSystemPlatform(),
"distutil.util.get_platform")
def testExecute(self):
EDTestCasePluginExecuteControlGridScreeningv1_0.testExecute(self)
edPlugin = self.getPlugin()
# Check that we have the image quality indicators
xsDataResult = edPlugin.getDataOutput()
EDAssert.equal(False,
xsDataResult.getImageQualityIndicators() is None,
"Result contains image quality indicators")
# Check that we don't have the indexing result
EDAssert.equal(True,
xsDataResult.getMosaicity() is None,
"Result doesn't contain the mosaicity estimation")
def testGenerateMOSFLMCommands(self):
"""
"""
pluginIndexing = self.createPlugin()
pluginIndexing.setScriptExecutable("cat")
pluginIndexing.configure()
xsDataMOSFLMInputIndexing = self.generateDataMOSFLMInputIndexing()
pluginIndexing.setDataInput(xsDataMOSFLMInputIndexing)
pluginIndexing.generateMOSFLMCommands()
listCommandsReference = ['WAVELENGTH 0.934', 'DISTANCE 198.4', 'BEAM 102.5 104.7', 'DETECTOR ADSC', 'DIRECTORY ' + self.strDataImagePath, 'TEMPLATE ref-testscale_1_###.img', 'NEWMAT ' + pluginIndexing.getNewmatFileName(), 'AUTOINDEX DPS REFINE IMAGE 1 PHI 0.0 1.0', 'AUTOINDEX DPS REFINE IMAGE 2 PHI 90.0 91.0', 'GO', 'MOSAIC ESTIMATE 1', 'GO', 'MOSAIC ESTIMATE 2', 'GO']
listCommands = pluginIndexing.getListCommandExecution()
EDAssert.equal(listCommandsReference, listCommands)
self.cleanUp(pluginIndexing)
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
# plugin.synchronize()
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = self.XSDataResult.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()
EDAssert.equal(xsDataResultReference.marshal(), xsDataResultObtained.marshal(), "XML are the same")
def testExecuteActionClusterWithFailure(self):
"""
Test the EDActionCluster with actions ending in success
"""
edActionCluster = EDActionCluster()
for i in range(10):
edAction = EDActionSuccess()
edActionCluster.addAction(edAction)
edActionFailure = EDActionFailure()
edActionCluster.addAction(edActionFailure)
edActionCluster.executeSynchronous()
EDAssert.equal(True, edActionCluster.isFailure(),
"EDActionCluster ended in failure")
def testExecute(self):
"""
Runs the plugin and then compares expected output with obtained output to verify that it executed correctly.
"""
self.run()
# Check that the id extists in the results
edPlugin = self.getPlugin()
xsDataResult = edPlugin.getDataOutput()
bAttributeExists = True
if xsDataResult.workflowId is None:
bAttributeExists = False
EDAssert.equal(True, bAttributeExists, "Attribute workflowId in the result")
def testInitaliseLabelitCommandLine(self):
"""
This method tests the initaliseLabelitCommandLine method of the Labelit plugin.
"""
edPluginLabelitv1_1 = self.createPlugin()
xmlInput1 = EDUtilsFile.readFile(self.__strReferenceInputFile1)
edPluginLabelitv1_1.setDataInput(xmlInput1, "referenceImage")
xmlInput2 = EDUtilsFile.readFile(self.__strReferenceInputFile2)
edPluginLabelitv1_1.setDataInput(xmlInput2, "referenceImage")
edPluginLabelitv1_1.initaliseLabelitCommandLine()
strScriptCommandLine = edPluginLabelitv1_1.getScriptCommandline()
strCommandLineExpected = "--index_only ${EDNA_TESTIMAGES}/images/ref-testscale_1_001.img ${EDNA_TESTIMAGES}/images/ref-testscale_1_002.img"
EDAssert.equal(strCommandLineExpected, strScriptCommandLine)
def testExecute(self):
"""
execute the execution test
"""
self.run()
# Checks the expected result
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
strObtainedOutput = self.readAndParseFile (self.m_edObtainedOutputDataFile)
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultExecCommandLine.parseString(strExpectedOutput)
xsDataResultObtained = XSDataResultExecCommandLine.parseString(strObtainedOutput)
EDAssert.equal(xsDataResultReference.marshal(), xsDataResultObtained.marshal())
def testExecute(self):
"""
"""
self.run()
plugin = self.getPlugin()
# Checking obtained results
xsDataResult = plugin.getDataOutput()
ref = self.readAndParseFile(self.getReferenceDataOutputFile())
obt = xsDataResult.marshal()
# EDVerbose.DEBUG("Reference: %s" % ref)
# EDVerbose.DEBUG("Obtained: %s" % obt)
EDAssert.equal(ref, obt, "XML object comparison")
def testGetXSDataResultBest4(self):
edPluginBest = self.createPlugin()
xsDataInputBest = XSDataInputBest()
edPluginBest.dataInput = xsDataInputBest
# Test 1
xsDataResultBest = edPluginBest.getXSDataResultBest(
os.path.join(self.strDataPath, "unit_test_4_best.log"))
xsDataResultBestReference = XSDataResultBest.parseFile(
os.path.join(self.strDataPath, "XSDataResultBest_unit_test_4.xml"))
print xsDataResultBest.marshal()
EDAssert.equal(xsDataResultBestReference.collectionPlan[0].marshal(),
xsDataResultBest.collectionPlan[0].marshal(),
"Collection plan")
def unitTestGetSIValue(self):
"""
test the execution of unitTestGetSIValue static method
"""
EDVerbose.DEBUG("EDTestCaseEDUtilsUnit.unitTestGetSIValue")
xsd = XSDataLength(1.5)
xsd.setUnit(XSDataString("mm"))
EDAssert.equal(0.0015, EDUtilsUnit.getSIValue(xsd),
"Conversion mm to meter")
xsd = XSDataAngle(90)
xsd.setUnit(XSDataString("deg"))
EDAssert.equal(math.pi / 2, EDUtilsUnit.getSIValue(xsd),
"Conversion deg to rad")
def testWriteDataOutput(self):
# Test 1: default Output with XML
edPlugin = EDPlugin()
edPlugin.configure()
xsDataStringTest = XSDataString("Test")
edPlugin.setDataOutput(xsDataStringTest)
edPlugin.writeDataOutput()
EDAssert.equal(True, os.path.exists(os.path.join(edPlugin.getWorkingDirectory(), "_dataOutput.xml")), "Test 1: default Output with XML")
# Test 2: named Output with XML
edPlugin = EDPlugin()
edPlugin.configure()
xsDataStringTest = XSDataString("Test")
edPlugin.setDataOutput(xsDataStringTest, "testData")
edPlugin.writeDataOutput()
EDAssert.equal(True, os.path.exists(os.path.join(edPlugin.getWorkingDirectory(), "_testData_0_dataOutput.xml")), "Test 2: named Output with XML")
# Test 3: several Outputs with the same name, XML Output
edPlugin = EDPlugin()
edPlugin.configure()
xsDataStringTest1 = XSDataString("Test1")
xsDataStringTest2 = XSDataString("Test2")
edPlugin.setDataOutput(xsDataStringTest1, "testData")
edPlugin.setDataOutput(xsDataStringTest2, "testData")
edPlugin.writeDataOutput()
EDAssert.equal(True, os.path.exists(os.path.join(edPlugin.getWorkingDirectory(), "_testData_0_dataOutput.xml")), "Test 3: several Outputs with the same name, XML Output, 1")
EDAssert.equal(True, os.path.exists(os.path.join(edPlugin.getWorkingDirectory(), "_testData_1_dataOutput.xml")), "Test 3: several Outputs with the same name, XML Output, 2")
def testExecute(self):
EDTestCasePluginExecuteControlCharacterisationv1_1.testExecute(self)
plugin = self.getPlugin()
xsDataCharacterisation = plugin.getDataOutput()
xsDataCollectionPlanList = xsDataCharacterisation.getStrategyResult(
).getCollectionPlan()
EDAssert.equal(2, len(xsDataCollectionPlanList))
strRankingResolutionInitial = xsDataCollectionPlanList[
1].getStrategySummary().getResolutionReasoning().getValue()
EDAssert.equal(
"Resolution limit is set by the initial image resolution",
strRankingResolutionInitial)
#Ric: to avoid error:
strRankingResolutionLow = xsDataCollectionPlanList[
0].getStrategySummary().getResolutionReasoning().getValue()
if (plugin.getPluginStrategyName == "EDPluginControlStrategyv1_1"):
EDAssert.equal("Low-resolution pass, no overloads",
strRankingResolutionLow)
elif (plugin.getPluginStrategyName == "EDPluginControlStrategyv1_2"):
EDAssert.equal(
"Low-resolution pass, no overloads and full completeness",
strRankingResolutionLow)
def testGetEdnaUserTempFolder(self):
# Test that we can access the user temp folder
strUserTempFolder = EDUtilsPath.getEdnaUserTempFolder()
EDAssert.equal(True, os.path.exists(strUserTempFolder),
"Checking that user temp folder exists")
# Test if we can write to the temp folder
strTest = "This is a test string."
strPathTestFile = os.path.join(strUserTempFolder,
"EDTestCaseEDUtilsPath_testFile.txt")
EDUtilsFile.writeFile(strPathTestFile, strTest)
EDAssert.equal(True, os.path.exists(strPathTestFile),
"Checking that new temp file exists")
# Delete the test file
os.remove(strPathTestFile)
def testInitaliseLabelitCommandLine(self):
"""
This method tests the initaliseLabelitCommandLine method of the Labelit plugin.
"""
edPluginLabelitv10 = self.createPlugin()
strReferenceInputFile = os.path.join(
self.getPluginTestsDataHome(),
"XSDataInputLabelit_testCommandLine.xml")
xmlInput = self.readAndParseFile(strReferenceInputFile)
edPluginLabelitv10.setDataInput(xmlInput)
edPluginLabelitv10.initaliseLabelitCommandLine()
strScriptCommandLine = edPluginLabelitv10.getScriptCommandline()
strCommandLineExpected = "--index_only images/ref-testscale_1_001.img images/ref-testscale_1_002.img"
EDAssert.equal(strCommandLineExpected, strScriptCommandLine)
def testExecute( self ):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
EDVerbose.DEBUG("Checking error messages...")
EDAssert.equal( self.m_iNoErrorMessages, self.getErrorMessages().getNumberObjects() )
EDVerbose.DEBUG("Checking warning messages...")
EDAssert.equal( self.m_iNoWarningMessages, self.getWarningMessages().getNumberObjects() )
def testExecute(self):
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
# Checks the expected result
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultControlISPyB = plugin.dataOutput
bExistScreeningId = False
if xsDataResultControlISPyB.screeningId is not None:
bExistScreeningId = True
EDAssert.equal(True, bExistScreeningId, "Screening id generated")
def testExecute(self):
EDTestCasePluginExecuteControlCharacterisationv1_3.testExecute(self)
edPlugin = self.getPlugin()
strStatusMessage = None
if edPlugin.hasDataOutput("statusMessage"):
strStatusMessage = edPlugin.getDataOutput(
"statusMessage")[0].getValue()
EDAssert.equal(True,
strStatusMessage.find("Indexing FAILURE") != -1,
"Status message contains 'Indexing FAILURE'")
edPlugin.generateExecutiveSummary(edPlugin)
edPlugin.verboseScreenExecutiveSummary()
def testWriteDataInput(self):
# Test 1: default input with XML
edPlugin = EDPlugin()
edPlugin.configure()
edPlugin.setXSDataInputClass(XSDataString)
xsDataStringTest = XSDataString("Test")
edPlugin.setDataInput(xsDataStringTest.marshal())
edPlugin.writeDataInput()
EDAssert.equal(True, os.path.exists(os.path.join(edPlugin.getWorkingDirectory(), "_dataInput.xml")), "Test 1: default input with XML")
# Test 2: named input with XML
edPlugin = EDPlugin()
edPlugin.configure()
edPlugin.setXSDataInputClass(XSDataString, "testData")
xsDataStringTest = XSDataString("Test")
edPlugin.setDataInput(xsDataStringTest.marshal(), "testData")
edPlugin.writeDataInput()
EDAssert.equal(True, os.path.exists(os.path.join(edPlugin.getWorkingDirectory(), "_testData_0_dataInput.xml")), "Test 2: named input with XML")
# Test 3: several inputs with the same name, XML input
edPlugin = EDPlugin()
edPlugin.configure()
edPlugin.setXSDataInputClass(XSDataString, "testData")
xsDataStringTest1 = XSDataString("Test1")
xsDataStringTest2 = XSDataString("Test2")
edPlugin.setDataInput(xsDataStringTest1.marshal(), "testData")
edPlugin.setDataInput(xsDataStringTest2.marshal(), "testData")
edPlugin.writeDataInput()
EDAssert.equal(True, os.path.exists(os.path.join(edPlugin.getWorkingDirectory(), "_testData_0_dataInput.xml")), "Test 3: several inputs with the same name, XML input, 1")
EDAssert.equal(True, os.path.exists(os.path.join(edPlugin.getWorkingDirectory(), "_testData_1_dataInput.xml")), "Test 3: several inputs with the same name, XML input, 2")
def testParseParameterFile(self):
edPluginControlID11 = self.createPlugin()
# Path to test parameter file
strDataPath = self.getPluginTestsDataHome()
strTestParameterFile = "id11_parameterFile_reference.txt"
strPath = os.path.join(strDataPath, strTestParameterFile)
dictID11 = edPluginControlID11.parseParameterFiles(strPath)
# dictSub = os.environ.copy()
# dictSub["TEST_DATA_IMAGES_HOME"] = EDUtilsTest.getTestsDataImagesHome()
# for keyId11 in dictID11:
# for key in dictSub:
# dictID11[keyId11] = dictID11[keyId11].replace("${%s}" % key , dictSub[ key ])
EDAssert.equal(self.dictID11Reference, dictID11,
"Dictionaries are the same")
def testGetProjectRootDirectory(self):
edFactoryPluginTest = EDFactoryPluginTest()
strEdnaHome = EDUtilsPath.getEdnaHome()
strTestProjectRootDirectoryReference = EDUtilsPath.appendListOfPaths(
strEdnaHome,
["kernel", "tests", "data", "EDFactoryPlugin", "testProject"])
strTestProjectRootDirectory1 = edFactoryPluginTest.getProjectRootDirectory(
"EDTestCasePluginUnitTestPluginFactory")
EDAssert.equal(strTestProjectRootDirectoryReference,
strTestProjectRootDirectory1)
strTestProjectRootDirectory2 = edFactoryPluginTest.getProjectRootDirectory(
"EDTestSuitePluginUnitTestProject")
EDAssert.equal(strTestProjectRootDirectoryReference,
strTestProjectRootDirectory2)
def testExecute(self):
# Start a timer for copying the file
pyTimer = Timer(5, self.copyFile)
pyTimer.start()
self.run()
pyTimer.cancel()
# Check timeout
edPlugin = self.getPlugin()
EDAssert.equal(False, edPlugin.dataOutput.timedOut.value,
"TimedOut should be False")
time.sleep(1)
shutil.rmtree(self.strTmpDir)
if self.strTmpDirOrig is not None:
os.environ["EDNA_TMP_DIR"] = self.strTmpDirOrig
