def testRasterConfiguration(self):
strPathToTestConfigFile = os.path.join(self.strUnitTestDataHome,
"XSConfiguration_raster.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(self.getPluginName())
xsDataMOSFLMInput = XSDataMOSFLMInput()
xsDataMOSFLMBeam = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeam.setX(XSDataLength(1.0))
xsDataMOSFLMBeam.setY(XSDataLength(2.0))
xsDataMOSFLMInput.setBeam(xsDataMOSFLMBeam)
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
xsDataMOSFLMInput.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInput.setDirectory(XSDataString("/tmp"))
xsDataMOSFLMInput.setTemplate(XSDataString("testdata_1_###.img"))
xsDataMOSFLMInput.setWavelength(XSDataWavelength(1.1111))
xsDataMOSFLMInput.setDistance(XSDataLength(222.22))
edPluginMOSFLMv10 = self.createPlugin()
edPluginMOSFLMv10.setScriptExecutable("cat")
edPluginMOSFLMv10.setConfig(dictItem, _bLocal=True)
edPluginMOSFLMv10.configure()
edPluginMOSFLMv10.setXSDataInputClass(XSDataMOSFLMInput)
edPluginMOSFLMv10.setDataInput(xsDataMOSFLMInput)
edPluginMOSFLMv10.generateMOSFLMCommands()
edListCommands = edPluginMOSFLMv10.getListCommandExecution()
edListCommandsReference = [
'WAVELENGTH 1.1111', 'DISTANCE 222.22', 'BEAM 1.0 2.0',
'DETECTOR ADSC', 'DIRECTORY /tmp', 'TEMPLATE testdata_1_###.img',
'RASTER 15 15 3 3 3'
]
EDAssert.equal(edListCommandsReference, edListCommands,
"MOSFLM commands with ratser configured")
def testRasterConfiguration(self):
strPathToTestConfigFile = os.path.join(self.strUnitTestDataHome, "XSConfiguration_raster.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(self.getPluginName())
xsDataMOSFLMInput = XSDataMOSFLMInput()
xsDataMOSFLMBeam = XSDataMOSFLMBeamPosition()
xsDataMOSFLMBeam.setX(XSDataLength(1.0))
xsDataMOSFLMBeam.setY(XSDataLength(2.0))
xsDataMOSFLMInput.setBeam(xsDataMOSFLMBeam)
xsDataMOSFLMDetector = XSDataMOSFLMDetector()
xsDataMOSFLMDetector.setType(XSDataString("ADSC"))
xsDataMOSFLMInput.setDetector(xsDataMOSFLMDetector)
xsDataMOSFLMInput.setDirectory(XSDataString("/tmp"))
xsDataMOSFLMInput.setTemplate(XSDataString("testdata_1_###.img"))
xsDataMOSFLMInput.setWavelength(XSDataWavelength(1.1111))
xsDataMOSFLMInput.setDistance(XSDataLength(222.22))
edPluginMOSFLMv10 = self.createPlugin()
edPluginMOSFLMv10.setScriptExecutable("cat")
edPluginMOSFLMv10.setConfig(dictItem, _bLocal = True)
edPluginMOSFLMv10.configure()
edPluginMOSFLMv10.setXSDataInputClass(XSDataMOSFLMInput)
edPluginMOSFLMv10.setDataInput(xsDataMOSFLMInput)
edPluginMOSFLMv10.generateMOSFLMCommands()
edListCommands = edPluginMOSFLMv10.getListCommandExecution()
edListCommandsReference = ['WAVELENGTH 1.1111', 'DISTANCE 222.22', 'BEAM 1.0 2.0', 'DETECTOR ADSC', 'DIRECTORY /tmp', 'TEMPLATE testdata_1_###.img', 'RASTER 15 15 3 3 3']
EDAssert.equal(edListCommandsReference, edListCommands, "MOSFLM commands with ratser configured")
def testConfigureOK(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
def testConfigureOK(self):
edPluginControlIndexingv10 = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginControlIndexingv10.getPluginName())
edPluginControlIndexingv10.setConfig(dictItem)
edPluginControlIndexingv10.configure()
def testSetDataModelInput(self):
edPluginBest = self.createPlugin()
edConfigurationGood01 = EDConfiguration(os.path.join(self.m_pyStrDataPath, "XSConfiguration.xml"))
dictItemGood01 = edConfigurationGood01.get(self.getPluginName())
edPluginBest.setConfig(dictItemGood01, _bLocal = True)
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 XSDataAngularSpeed
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(XSDataAngularSpeed(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(os.path.join(self.m_pyStrDataPath, "bestfile.dat"))
xsDataInputBest.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.m_pyStrDataPath, "bestfile.par"))
xsDataInputBest.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.m_pyStrDataPath, "bestfile1.hkl"))
xsDataInputBest.addBestFileContentHKL(XSDataString(bestFileContentHKL))
xsDataInputBest.exportToFile(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 testConfigureOK(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
EDAssert.equal("/opt/pxsoft/ccp4-6.0.2/lib/data", edPluginStrategy.getSymopHome())
def testConfigureOK(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(),
"XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(),
"XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
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:
self.unitTest(heavyAtom.getSymbol().getValue() + " : " +
str(heavyAtom.getNumberOf().getValue()))
if (heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def testConfigureOK(self):
edPluginRaddose = self.createPlugin()
edConfigurationGood01 = EDConfiguration(os.path.join(self.strDataPath, "XSConfiguration.xml"))
dictItemGood01 = edConfigurationGood01.get(self.getPluginName())
edPluginRaddose.setConfig(dictItemGood01, _bLocal = True)
edPluginRaddose.setScriptExecutable("cat")
edPluginRaddose.configure()
EDAssert.equal("/bin/bash", edPluginRaddose.getScriptShell())
EDAssert.equal("cat", edPluginRaddose.getScriptExecutable())
EDAssert.equal("/opt/pxsoft/ccp4-6.0.2/include/ccp4.setup-bash.orig", edPluginRaddose.getSetupCCP4())
EDAssert.equal("Verion of Raddose to be tested", edPluginRaddose.getStringVersion())
#EDAssert.equal(600, edPluginMessage.getTimeOut())
self.cleanUp(edPluginRaddose)
def testGenerateMOSFLMIntegrationCommands(self):
strPathToTestConfigFile = os.path.join(self.strUnitTestDataHome, "XSConfiguration_unitTest.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(self.getPluginName())
pluginIntegration = self.createPlugin()
pluginIntegration.setScriptExecutable("cat")
pluginIntegration.setConfig(dictItem, _bLocal = True)
pluginIntegration.configure()
strXMLInputData = self.readAndParseFile (self.strReferenceDataInputFile)
pluginIntegration.setDataInput(strXMLInputData)
pluginIntegration.generateMOSFLMCommands()
listCommandExecution = pluginIntegration.getListCommandExecution()
listCommandReference = ['WAVELENGTH 0.934', 'DISTANCE 198.440994', 'BEAM 102.478996 104.8862', 'DETECTOR ADSC', 'DIRECTORY ' + self.strDataImagePath, 'TEMPLATE ref-testscale_1_###.img', 'SYMMETRY P222', 'MATRIX ' + pluginIntegration.getScriptBaseName() + '_matrix.mat', 'MOSAIC 0.75', 'HKLOUT process_1_1.mtz', 'PROCESS 1 TO 1 START 0.000000 ANGLE 1.000000', 'BEST ON', 'GO', 'BEST OFF']
EDAssert.equal(listCommandReference, listCommandExecution)
def testSetDataInput(self):
edPluginControlIntegrationv10 = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginControlIntegrationv10.getPluginName())
edPluginControlIntegrationv10.setConfig(dictItem)
edPluginControlIntegrationv10.configure()
xmlInputReference = self.readAndParseFile(self.strReferenceInputFile)
from XSDataMXv1 import XSDataIntegrationInput
xsDataIntegrationInputReference = XSDataIntegrationInput.parseString(xmlInputReference)
edPluginControlIntegrationv10.setDataInput(xmlInputReference)
xsDataIntegrationv10Input = edPluginControlIntegrationv10.getDataInput()
EDAssert.equal(xsDataIntegrationInputReference.marshal(), xsDataIntegrationv10Input.marshal())
self.cleanUp(edPluginControlIntegrationv10)
def testConfigureOK(self):
edPluginBest = self.createPlugin()
edConfigurationGood01 = EDConfiguration(os.path.join(self.m_pyStrDataPath, "XSConfiguration.xml"))
dictItemGood01 = edConfigurationGood01.get(self.getPluginName())
edPluginBest.setConfig(dictItemGood01, _bLocal = True)
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, edPluginBest.getTimeOut())
EDAssert.equal("/home/sweet/home", edPluginBest.getBestHome())
EDAssert.equal("export besthome=/home/sweet/home", edPluginBest.getCommandBestHome())
self.cleanUp(edPluginBest)
def testSetDataInput(self):
edPluginControlIndexingv10 = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginControlIndexingv10.getPluginName())
edPluginControlIndexingv10.setConfig(dictItem)
edPluginControlIndexingv10.configure()
xmlInput = self.readAndParseFile(self.__strReferenceInputFile)
edPluginControlIndexingv10.setDataInput(xmlInput)
xsDataIndexingv01Input = edPluginControlIndexingv10.getDataInput()
xsDataIndexingInputReference = XSDataIndexingInput.parseString(xmlInput)
EDAssert.equal(xsDataIndexingInputReference.marshal(), xsDataIndexingv01Input.marshal())
self.cleanUp(edPluginControlIndexingv10)
def testConfigureOK(self):
edPluginRaddose = self.createPlugin()
edConfigurationGood01 = EDConfiguration(
os.path.join(self.strDataPath, "XSConfiguration.xml"))
dictItemGood01 = edConfigurationGood01.get(self.getPluginName())
edPluginRaddose.setConfig(dictItemGood01, _bLocal=True)
edPluginRaddose.setScriptExecutable("cat")
edPluginRaddose.configure()
EDAssert.equal("/bin/bash", edPluginRaddose.getScriptShell())
EDAssert.equal("cat", edPluginRaddose.getScriptExecutable())
EDAssert.equal("/opt/pxsoft/ccp4-6.0.2/include/ccp4.setup-bash.orig",
edPluginRaddose.getSetupCCP4())
EDAssert.equal("Verion of Raddose to be tested",
edPluginRaddose.getStringVersion())
#EDAssert.equal(600, edPluginMessage.getTimeOut())
self.cleanUp(edPluginRaddose)
def testConfigureOK(self):
edPluginBest = self.createPlugin()
edConfigurationGood01 = EDConfiguration(
os.path.join(self.strDataPath, "XSConfiguration.xml"))
dictItemGood01 = edConfigurationGood01.get(self.getPluginName())
edPluginBest.setConfig(dictItemGood01, _bLocal=True)
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, edPluginBest.getTimeOut())
EDAssert.equal("/home/sweet/home", edPluginBest.getBestHome())
EDAssert.equal("export besthome=/home/sweet/home",
edPluginBest.getCommandBestHome())
self.cleanUp(edPluginBest)
def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
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:
self.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if(heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def testGenerateMOSFLMIntegrationCommands(self):
strPathToTestConfigFile = os.path.join(self.strUnitTestDataHome,
"XSConfiguration_unitTest.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(self.getPluginName())
pluginIntegration = self.createPlugin()
pluginIntegration.setScriptExecutable("cat")
pluginIntegration.setConfig(dictItem, _bLocal=True)
pluginIntegration.configure()
strXMLInputData = self.readAndParseFile(self.strReferenceDataInputFile)
pluginIntegration.setDataInput(strXMLInputData)
pluginIntegration.generateMOSFLMCommands()
listCommandExecution = pluginIntegration.getListCommandExecution()
listCommandReference = [
'WAVELENGTH 0.934', 'DISTANCE 198.440994',
'BEAM 102.478996 104.8862', 'DETECTOR ADSC',
'DIRECTORY ' + self.strDataImagePath,
'TEMPLATE ref-testscale_1_###.img', 'SYMMETRY P222',
'MATRIX ' + pluginIntegration.getScriptBaseName() + '_matrix.mat',
'MOSAIC 0.75', 'HKLOUT process_1_1.mtz',
'PROCESS 1 TO 1 START 0.000000 ANGLE 1.000000', 'BEST ON', 'GO',
'BEST OFF'
]
EDAssert.equal(listCommandReference, listCommandExecution)
class EDPlugin(EDAction):
"""
This is the EDNA plugin main class
An EDNA plugin class:
- is a configurable entity
- has a base name (<date>-<random number>-<base name>)
- handles input/output data (setter, getter, checker)
- has warning and error messages
- has a base and a working directory (both are configurable)
The working directory is the folder from which the plugin is launched
and should contain all associated files with the plugin execution (edna xml input/output, 3rd party output files)
The base directory is the parent directory of the working directory.
Example: the working directory of a control plugin is the base directory of the plugins that it invokes,
i.e. the plugins working directories has the control plugin working directory as parent.
- defines the method that generates an executive summary (user-related output summary) that sub-classes should implement
"""
CONF_BASE_DIR_LABEL = "baseDirectory"
CONF_WORKING_DIR_LABEL = "workingDirectory"
CONF_TIME_OUT = "timeOut"
CONF_WRITE_XML_INPUT_OUTPUT = "writeXMLInputOutput"
CONF_WRITE_XML_OUTPUT = "writeXMLOutput"
CONF_WRITE_XML_INPUT = "writeXMLInput"
def __init__ (self):
"""
Initializes plugin related attributes described above
"""
EDAction.__init__(self)
self.__xsPluginItem = None
self.__dictXSDataInputClass = {}
self.__dictXSDataInput = {}
self.__dictXSDataOutput = {}
self.__strDefaultInputDataKey = "defaultInputData"
self.__strDefaultOutputDataKey = "defaultOutputData"
self.__edSlotExportDataOutput = EDSlot()
self.__strBaseDirectory = None
self.__strWorkingDirectory = None
self.__strBaseName = None
self.__listExecutiveSummaryLines = []
self.__strExecutiveSummarySeparator = "-" * 80
self.__listErrorMessages = []
self.__listWarningMessages = []
self.__isRequiredToHaveConfiguration = False
self.__bWriteDataXMLInputOutput = True
self.__bWriteDataXMLOutput = True
self.__bWriteDataXMLInput = True
self.__strPluginId = "%s-%08i" % (self.getClassName(), self.getId())
self.strPathDataInput = None
self.strPathDataOutput = None
self.__bUseWarningInsteadOfError = False
self.__edConfiguration = EDConfigurationStatic()
def preProcess(self, _edObject=None):
"""
Writes xml data input in the working dir (if required)
Connects a slot for generating the executive summary after the plugin execution
Connects a slot for checking output data to the finally process
Initialize the base directory
Configures the plugin
Checks the input data
"""
EDAction.preProcess(self, _edObject)
self.DEBUG("EDPlugin.preProcess")
self.connectPostProcess(self.exportDataOutput)
if self.__bWriteDataXMLInputOutput:
if self.__bWriteDataXMLInput:
self.connectPreProcess(self.writeDataInput)
self.connectPostProcess(self.generateExecutiveSummary)
self.connectFinallyProcess(self.checkDataOutput)
if (self.__strBaseName is None):
self.setBaseName(self.createBaseName())
EDStatus.tellRunning(self.__strPluginId)
self.connectFinallyProcess(self.tellFinished)
self.checkParameters()
def tellFinished(self, _edObject=None):
"""
Tell EDStatus that the plugin has finished, either in success either in error
"""
if self.isFailure():
EDStatus.tellFailure(self.__strPluginId)
else:
EDStatus.tellSuccess(self.__strPluginId)
def checkDataOutput(self, _edObject=None):
"""
Checks if output data is available, if not issues a warning and sets an empty XSDataResult as output data
Writes xml data output in the working dir (if required)
"""
EDAction.finallyProcess(self, _edObject)
if self.__dictXSDataOutput == {}:
strWarningMessage = "Output data for plugin %s not set, using XSDataResult as output" % self.getPluginName()
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self.setDataOutput(XSDataResult())
if self.__bWriteDataXMLInputOutput:
if self.__bWriteDataXMLOutput:
self.writeDataOutput()
def synchronize(self):
"""
This method calls EDAction.synchronize and if a time-out occurs an error message
is added to the list of error messages.
"""
EDAction.synchronize(self)
if self.isTimeOut():
strErrorMessage = "Timeout when waiting for %s to terminate." % self.getClassName()
self.addErrorMessage(strErrorMessage)
def getConfig(self):
"""
Gets the Plugin Configuration as a dictionary
"""
# self.DEBUG("EDPlugin.getConfig")
return self.__edConfiguration.get(self.getPluginName(), {})
def setConfig(self, _dict, _bLocal=False):
"""
Receives a dictionary (Plugin Configuration) from the application.
"""
self.DEBUG("EDPlugin.setConfiguration")
if _bLocal:
self.__edConfiguration = EDConfiguration()
if _dict is not None:
self.__edConfiguration[self.getPluginName()] = _dict
else:
self.__edConfiguration[self.getPluginName()] = {}
config = property(getConfig, setConfig)
def configure(self):
"""
Should be overridden by the Final Plugin If needed
This method should set its proper members attributes from a Plugin configuration Object
"""
self.DEBUG("EDPlugin.configure : plugin name = %s, EDNA_SITE = %s" % (self.getPluginName(), EDUtilsPath.EDNA_SITE))
# set Timeout if different from default one
if self.getTimeOut() == self.getDefaultTimeOut():
# Try to get time out from plugin configuration
iTimeOut = self.config.get(EDPlugin.CONF_TIME_OUT, None)
if iTimeOut is not None:
self.DEBUG("EDPlugin.configure: Setting time out to %d s from plugin configuration." % iTimeOut)
self.setTimeOut(iTimeOut)
else:
self.DEBUG("EDPlugin.configure: timeout already set before plugin is configured.")
# Base directory
strBaseDirectory = self.getBaseDirectory()
if (strBaseDirectory is None):
# Try to get base directory from plugin configuration
strBaseDirectory = self.config.get(EDPlugin.CONF_BASE_DIR_LABEL, None)
if(strBaseDirectory is None):
# Try to get working directory from environment variable
strBaseDirectory = os.environ.get("EDNA_BASE_DIRECTORY")
if (strBaseDirectory is None):
self.DEBUG("EDPlugin.configure: Using current base directory as working directory.")
strBaseDirectory = os.getcwd()
else:
self.DEBUG("EDPlugin.configure: Setting base directory from $EDNA_WORKING_DIRECTORY.")
else:
if (strBaseDirectory == "."):
self.DEBUG("EDPlugin.configure: Using current base directory as working directory.")
strBaseDirectory = os.getcwd()
else:
strBaseDirectory = os.path.abspath(strBaseDirectory)
self.DEBUG("EDPlugin.configure: Setting base directory from plugin configuration.")
self.setBaseDirectory(strBaseDirectory)
else:
self.DEBUG("EDPlugin.configure: Base directory already set before plugin is configured.")
# Working directory
strWorkingDirectory = self.getWorkingDirectory()
if (strWorkingDirectory is None):
# Try to get working directory from plugin configuration
strWorkingDirectory = self.config.get(EDPlugin.CONF_WORKING_DIR_LABEL, None)
if(strWorkingDirectory is not None):
self.DEBUG("EDPlugin.configure: Setting working directory from plugin configuration.")
else:
self.DEBUG("EDPlugin.configure: Setting working directory as base directory + base name.")
strWorkingDirectory = os.path.join(self.getBaseDirectory(), self.getBaseName())
self.setWorkingDirectory(strWorkingDirectory)
else:
self.DEBUG("EDPlugin.configure: Working directory already set before plugin is configured.")
#
self.__bWriteDataXMLInputOutput = bool(self.config.get(self.CONF_WRITE_XML_INPUT_OUTPUT, True))
self.__bWriteDataXMLOutput = bool(self.config.get(self.CONF_WRITE_XML_OUTPUT, True))
self.__bWriteDataXMLInput = bool(self.config.get(self.CONF_WRITE_XML_INPUT, True))
def execute(self, _edObject=None):
# Configure the plugin before starting it's thread
self.configure()
EDAction.execute(self, _edObject)
def checkParameters(self):
"""
Should be overridden by the Final Plugin If needed
This method should check that the data input are consistent
"""
self.DEBUG("EDPlugin.checkParameters")
def setXSDataInputClass(self, _xsDataInputClass, _strDataInputKey=None):
"""
This method should be called in the constructor of the derived plugins
in order to set the XSData type of the input data, e.g. XSDataInputXXX
"""
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInputClass.keys()):
strErrorMessage = "ERROR: " + self.getPluginName() + ".setXSDataInputClass, Data Input Class already defined for key: " + strDataInputKey
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
self.__dictXSDataInputClass[ strDataInputKey ] = _xsDataInputClass
def getXSDataInputClass(self, _strDataInputKey=None):
"""
Returns the XSData type of the input data.
"""
pyXSDataInputClass = None
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInputClass.keys()):
pyXSDataInputClass = self.__dictXSDataInputClass[ strDataInputKey ]
return pyXSDataInputClass
def setDataInput(self, _oDataInput, _strDataInputKey=None):
"""
Sets the plugin input data.
_oDataInput could be either an String XML or an XSData object.
The input data is stored in a dictionary with the key _strDataInputKey.
If the key is not provided a default key is used.
If not data input class is defined for the key an exception is raised.
If the key is not the default key, the data object is added to a list which
might contain already stored object(s).
If _oDataInput is None the list corresponding to a keyword is deleted.
"""
self.DEBUG("EDPlugin.setDataInput")
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
# Allow for None input
if (_oDataInput is None):
self.DEBUG("EDPlugin.setDataInput: Data input is None")
self.__dictXSDataInput[ strDataInputKey ] = []
elif (self.getXSDataInputClass(strDataInputKey) is None):
strErrorMessage = "ERROR: " + self.getPluginName() + ".setDataInput, Data Input Class not defined for key: " + strDataInputKey
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
# Check the type
xsDataInput = None
if isinstance(_oDataInput, (str, unicode)):
self.DEBUG("EDPlugin.setDataInput: Input Data is string ")
xsDataInput = self.getXSDataInputClass(strDataInputKey).parseString(_oDataInput)
elif (isinstance(_oDataInput, self.getXSDataInputClass(strDataInputKey))):
self.DEBUG("EDPlugin.setDataInput: Input Data is of type " + str(_oDataInput.__class__))
xsDataInput = _oDataInput
else:
strErrorMessage = "ERROR: %s.setDataInput, wrong data type %r for data input key: %s, expected XML string or %r" % \
(self.getPluginName(), _oDataInput.__class__, strDataInputKey, self.getXSDataInputClass(strDataInputKey))
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
# Add the object to a list if its key is not the default key
if (strDataInputKey != self.__strDefaultInputDataKey) :
# Check if there's already a list stored
if (not strDataInputKey in self.__dictXSDataInput.keys()):
self.__dictXSDataInput[ strDataInputKey ] = []
self.__dictXSDataInput[ strDataInputKey ].append(xsDataInput)
else:
self.__dictXSDataInput[ strDataInputKey ] = xsDataInput
def hasDataInput(self, _strDataInputKey=None):
"""
Returns True if the plugin has Input Data for a particular key.
If the key is not provided a default key is used.
"""
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInput.keys()):
return True
else:
return False
def getDataInput(self, _strDataInputKey=None):
"""
Returns the Plugin Input Data for a particular key.
If the key is not provided a default key is used.
"""
oValue = None
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInput.keys()):
oValue = self.__dictXSDataInput[ strDataInputKey ]
else:
strErrorMessage = self.getPluginName() + ".getDataInput, no input data defined for key: " + strDataInputKey
self.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
return oValue
def delDataInput(self, _strDataInputKey=None):
"""
Deletes the data input for a particular key.
If the key is not provided a default key is used.
"""
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInput.keys()):
self.__dictXSDataInput[ strDataInputKey ] = None
else:
strErrorMessage = self.getPluginName() + ".delDataInput, no input data defined for key: " + strDataInputKey
self.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
# Property for dataInput
dataInput = property(getDataInput, setDataInput, delDataInput, "Property for dataInput")
def setDataOutput(self, _xsDataOutput, _strDataOutputKey=None):
"""
Sets the plugin output data for a particular key.
If the key is not provided a default key is used.
If the key is already defined in the dictionary, the corresponding
data object is added to a list which contains the already stored object(s).
"""
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self.__strDefaultOutputDataKey
# Add the object to a list if its key not the default key
if (strDataOutputKey == self.__strDefaultOutputDataKey):
self.__dictXSDataOutput[ strDataOutputKey ] = _xsDataOutput
else:
# Check if the _xsDataoutput object is already a list
if (type(_xsDataOutput) == list):
self.__dictXSDataOutput[ strDataOutputKey ] = _xsDataOutput
else:
# Check if the stored object contains already a list
if (not strDataOutputKey in self.__dictXSDataOutput.keys()):
self.__dictXSDataOutput[ strDataOutputKey ] = []
self.__dictXSDataOutput[ strDataOutputKey ].append(_xsDataOutput)
def getDataOutput(self, _strDataOutputKey=None):
"""
Returns the Plugin Output Data
"""
oValue = None
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self.__strDefaultOutputDataKey
if (strDataOutputKey in self.__dictXSDataOutput.keys()):
oValue = self.__dictXSDataOutput[ strDataOutputKey ]
return oValue
def hasDataOutput(self, _strDataOutputKey=None):
"""
Returns True if the plugin has the specified Output Data
"""
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self.__strDefaultOutputDataKey
if (strDataOutputKey in self.__dictXSDataOutput.keys()):
return True
else:
return False
def delDataOutput(self, _strDataOutputKey=None):
"""
Deletes the data output for a particular key.
If the key is not provided a default key is used.
"""
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self.__strDefaultOutputDataKey
if (strDataOutputKey in self.__dictXSDataOutput.keys()):
self.__dictXSDataOutput[ strDataOutputKey ] = None
else:
strErrorMessage = self.getPluginName() + ".delDataOutput, no output data defined for key: " + _strDataOutputKey
self.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
# Property for dataOutput
dataOutput = property(getDataOutput, setDataOutput, delDataOutput, "Property for dataOutput")
def exportDataOutput(self, _edPlugin=None):
"""
Deprecated
Exports the Plugin Output Data to slot
"""
self.DEBUG("EDPlugin.exportDataOutput")
self.__edSlotExportDataOutput.call(self.__dictXSDataOutput)
def connectExportDataOutput(self, _oMethod):
"""
Deprecated
"""
self.synchronizeOn()
if (_oMethod != None):
self.__edSlotExportDataOutput.connect(_oMethod)
self.synchronizeOff()
def generateExecutiveSummary(self, _edPlugin):
"""
This method, which should be implemented by sub-classes, generates an executive summary (user-related output summary).
"""
self.DEBUG("EDPlugin.generateExecutiveSummary")
def addErrorMessage(self, _strErrorMessage):
"""
Adds an error message to the error messages list
"""
self.__listErrorMessages.append(_strErrorMessage)
def getListOfErrorMessages(self):
"""
Returns the error messages list
"""
return self.__listErrorMessages
def addWarningMessage(self, _strWarningMessage):
"""
Adds a warning message to the warning messages list
"""
self.DEBUG("EDPlugin.addWarningMessage : " + _strWarningMessage)
self.__listWarningMessages.append(_strWarningMessage)
def getListOfWarningMessages(self):
"""
Returns the warning messages list
"""
return self.__listWarningMessages
def writeDataInput(self, _edObject=None):
"""
Writes the input data object(s) into a working dir xml file
"""
self.DEBUG("EDPlugin.writeDataInput")
strBasename = os.path.join(self.getWorkingDirectory(), self.compactPluginName(self.getPluginName()))
for strKey in self.__dictXSDataInput.keys():
if (strKey == self.__strDefaultInputDataKey): # "Old" style
xsDataInput = self.__dictXSDataInput[ self.__strDefaultInputDataKey ]
self.strPathDataInput = strBasename + "_dataInput.xml"
EDUtilsFile.writeFile(self.strPathDataInput, xsDataInput.marshal())
else: # We have a list of objects
listXSDataInput = self.__dictXSDataInput[ strKey ]
for iIndex, xsDataInput in enumerate(listXSDataInput):
strPathDataInput = "%s_%s_%d_dataInput.xml" % (strBasename, strKey, iIndex)
EDUtilsFile.writeFile(strPathDataInput, xsDataInput.marshal())
def writeDataOutput(self, _edObject=None):
"""
Writes the output data object(s) into a working dir xml file
"""
self.DEBUG("EDPlugin.writeDataOutput")
for strKey in self.__dictXSDataOutput.keys():
if (strKey == self.__strDefaultOutputDataKey): # "Old" style
xsDataOutput = self.__dictXSDataOutput[ self.__strDefaultOutputDataKey ]
if (xsDataOutput is not None):
self.strPathDataOutput = os.path.join(self.getWorkingDirectory(), self.compactPluginName(self.getPluginName()) + "_dataOutput.xml")
EDUtilsFile.writeFile(self.strPathDataOutput, xsDataOutput.marshal())
else:
listXSDataOutput = self.__dictXSDataOutput[ strKey ]
for iIndex, xsDataOutput in enumerate(listXSDataOutput):
if (xsDataOutput is not None):
strPathDataOutput = os.path.join(self.getWorkingDirectory(), self.compactPluginName(self.getPluginName()) + "_" + strKey + "_%d_dataOutput.xml" % iIndex)
EDUtilsFile.writeFile(strPathDataOutput, xsDataOutput.marshal())
def getBaseName(self):
"""
Returns the plugin base name
"""
if (self.__strBaseName is None):
self.__strBaseName = self.createBaseName()
return self.__strBaseName
def setBaseName(self, _strBaseName):
"""
Sets the plugin base name
"""
self.__strBaseName = self.compactPluginName(_strBaseName)
self.setName(self.__strBaseName)
# Create the directory baseDirectory/baseName which will be used as working directory
strWorkingDirPath = os.path.join(self.getBaseDirectory(), self.__strBaseName)
if not os.path.isdir(strWorkingDirPath):
os.mkdir(strWorkingDirPath)
self.setWorkingDirectory(strWorkingDirPath)
def createBaseName(self):
"""
Generates the plugin base name: (<prefix>-<object ID>)
"""
# First try to use global instance ID from EDObject
strBaseName = "%s-%08d" % (self.compactPluginName(self.getPluginName()), self.getId())
strBaseDir = os.path.join(self.getBaseDirectory(), strBaseName)
# Try to create the directory...
try:
os.mkdir(strBaseDir)
except Exception as strErrorDetail:
self.error("EDPlugin.createBaseName: Could not create base directory %s because of %s" % (strBaseDir, strErrorDetail))
self.warning("EDPlugin.createBaseName: Trying to create alternative base directory...")
self.writeErrorTrace()
strTempDir = tempfile.mkdtemp(prefix=strBaseName, dir=self.getBaseDirectory())
os.chmod(strTempDir, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)
strBaseName = os.path.split(strTempDir)[1]
strBaseDir = os.path.join(self.getBaseDirectory(), strBaseName)
self.warning("EDPlugin.createBaseName: Alternative base directory created: %s" % strBaseDir)
self.DEBUG("EDPlugin.createBaseName : Directory created = " + strBaseDir)
return strBaseName
def compactPluginName(self, _pluginName):
"""
The prefix is constructed from the plugin name with the following renaming:
EDPlugin -> ""
EDPluginExec -> ""
EDPluginControl -> "Control"
"""
strCompactName = _pluginName
if (strCompactName.startswith("EDPluginExec")):
strCompactName = strCompactName[12:]
elif (strCompactName.startswith("EDPluginControl")):
strCompactName = strCompactName[8:]
elif (strCompactName.startswith("EDPlugin")):
strCompactName = strCompactName[8:]
return strCompactName
def setBaseDirectory(self, _strBaseDirectory):
"""
Sets the plugin base directory
"""
self.DEBUG("EDPlugin.setBaseDirectory : " + _strBaseDirectory)
if (not os.path.isdir(_strBaseDirectory)):
self.DEBUG("EDPlugin.setBaseDirectory: base directory %s does dot yet exist! Creating it." % _strBaseDirectory)
os.mkdir(_strBaseDirectory)
self.__strBaseDirectory = _strBaseDirectory
def getBaseDirectory(self):
"""
Returns the plugin base directory
"""
self.DEBUG("EDPlugin.getBaseDirectory : %s" % self.__strBaseDirectory)
if (self.__strBaseDirectory is None):
self.__strBaseDirectory = os.getcwd()
return self.__strBaseDirectory
def setWorkingDirectory(self, _strWorkingDirectory):
"""
Sets the plugin working directory
"""
self.DEBUG("EDPlugin.setWorkingDirectory : " + _strWorkingDirectory)
self.__strWorkingDirectory = _strWorkingDirectory
if not os.path.isdir(_strWorkingDirectory):
self.DEBUG("EDPlugin.setWorkingDirectory, creating working directory %s." % _strWorkingDirectory)
os.mkdir(self.__strWorkingDirectory)
def getWorkingDirectory(self):
"""
Returns the plugin base directory
"""
self.DEBUG("EDPlugin.getWorkingDirectory : %s" % self.__strWorkingDirectory)
returnValue = None
if (self.__strWorkingDirectory is not None):
returnValue = self.__strWorkingDirectory
return returnValue
def checkMandatoryParameters(self, _xsData, _strParamName):
"""
Checks that a mandatory parameter exists in the data
If not, an error message is added in the list and the plugin fails
"""
if _xsData is None or (hasattr(_xsData, '__len__') and len(_xsData) == 0):
strErrorMessage = "%s: input parameter is missing: %s" % (self.getPluginName(), _strParamName)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
def checkImportantParameters(self, _xsData, _strParamName):
"""
Checks that a specific parameter exists in the data
If not, a warning message is added in the list
"""
if(_xsData == None):
strWarningMessage = "%s: input parameter is missing: %s" % (self.getPluginName(), _strParamName)
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
def addExecutiveSummaryLine(self, _strExecutiveSummaryLine):
"""
Add a line to the executive summary string.
"""
self.DEBUG("EDPlugin.addExecutiveSummaryLine : %r" % _strExecutiveSummaryLine)
strExecutiveSummaryLine = _strExecutiveSummaryLine
if (not strExecutiveSummaryLine == ""):
if (strExecutiveSummaryLine[-1] == "\n"):
strExecutiveSummaryLine = strExecutiveSummaryLine[:-1]
self.__listExecutiveSummaryLines.append(strExecutiveSummaryLine)
def addExecutiveSummarySeparator(self, _strSeparator=None):
"""
Adds a separator to split the executive summary into different parts
Default is a dotted line
"""
strSeparator = _strSeparator
if (strSeparator is None):
strSeparator = self.__strExecutiveSummarySeparator
# Check that the last line doesn't already contain a separator
if self.__listExecutiveSummaryLines != []:
if self.__listExecutiveSummaryLines[-1] != strSeparator:
self.addExecutiveSummaryLine(strSeparator)
else:
self.addExecutiveSummaryLine(strSeparator)
def getListExecutiveSummaryLines(self):
"""
Returns the executive summary (list of text lines)
"""
return self.__listExecutiveSummaryLines
def verboseScreenExecutiveSummary(self):
"""
Prints the executive summary on the screen
"""
for line in self.getListExecutiveSummaryLines():
self.screen(line)
def verboseDebug(self, _strMessage):
self.DEBUG(self.getPluginName() + " : " + _strMessage)
def getPluginName(self):
return self.getClassName()
def getListOfDataInputKeys(self):
return self.__dictXSDataInput.keys()
def getListOfDataOutputKeys(self):
return self.__dictXSDataOutput.keys()
def getDefaultInputDataKey(self):
return self.__strDefaultInputDataKey
def getDefaultOutputDataKey(self):
return self.__strDefaultOutputDataKey
def getExecutiveSummarySeparator(self):
return self.__strExecutiveSummarySeparator
def isRequiredToHaveConfiguration(self):
"""
If the return value from this method is true, the plugin
is required to have a configuration in order to be executed in a
plugin execution test case.
@return: RequiredToHaveConfiguration
@rtype: boolean
"""
return self.__isRequiredToHaveConfiguration
def setRequiredToHaveConfiguration(self, _bValue=True):
"""
Sets or unsets the plugin to be required to have a configuration
for execution in a plugin execution test case.
plugin execution test case.
@param _bValue: RequiredToHaveConfiguration
@type: boolean
"""
self.__isRequiredToHaveConfiguration = _bValue
def setWriteXMLInputOutput(self, _bValue=True):
"""
Sets or unsets the plugin to write XML input and output files.
@param _bValue: WriteDataXMLInputOutput
@type: boolean
"""
self.__bWriteDataXMLInputOutput = _bValue
def setWriteXMLInput(self, _bValue=True):
"""
Sets or unsets the plugin to write XML input files.
@param _bValue: WriteDataXMLInput
@type: boolean
"""
self.__bWriteDataXMLInput = _bValue
def setWriteXMLOutput(self, _bValue=True):
"""
Sets or unsets the plugin to write XML output files.
@param _bValue: WriteDataXMLOutput
@type: boolean
"""
self.__bWriteDataXMLOutput = _bValue
def setUseWarningInsteadOfError(self, _bValue=True):
"""
Sets or unsets the plugin to use warning messages also for error messages.
@param _bValue: UseWarningInsteadOfError
@type: boolean
"""
self.__bUseWarningInsteadOfError = _bValue
def error(self, _strErrorMessage):
"""
Overloaded from EDLogging. If self.__bUseWarningInsteadOfError is True
a warning message is issued instead of an error message.
"""
if self.__bUseWarningInsteadOfError:
self.warning(_strErrorMessage)
else:
EDAction.error(self, _strErrorMessage)
def ERROR(self, _strErrorMessage):
"""
Uses the overloaded self.error method above.
"""
self.error(_strErrorMessage)
def testSetDataModelInput(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(),
"XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
xsDataStrategy = XSDataInputStrategy()
# Beam
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setWavelength(XSDataWavelength(2.41))
xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsBeam.setExposureTime(XSDataTime(1))
xsExperimentalCondition.setBeam(xsBeam)
# Detector and Exposure Time
xsDataDetector = XSDataDetector()
xsDataDetector.setType(XSDataString("q210-2x"))
xsExperimentalCondition.setDetector(xsDataDetector)
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setRotationAxis(XSDataString("phi"))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)
# Best Files
bestFileContentDat = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.dat"))
xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.par"))
xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile1.hkl"))
xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))
# Crystal
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataDouble(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(
XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
XSDataLength(0.1)))
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))
xsDataStrategy.setCrystalRefined(xsDataCrystal)
xsDataStrategy.setSample(xsDataSampleCrystalMM)
xsDataStrategy.exportToFile(self.strObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile(self.strObtainedInputFile)
xsDataInputExpected = XSDataInputStrategy.parseString(
pyStrExpectedInput)
xsDataInputObtained = XSDataInputStrategy.parseString(
pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
class EDPlugin(EDAction):
"""
This is the EDNA plugin main class
An EDNA plugin class:
- is a configurable entity
- has a base name (<date>-<random number>-<base name>)
- handles input/output data (setter, getter, checker)
- has warning and error messages
- has a base and a working directory (both are configurable)
The working directory is the folder from which the plugin is launched
and should contain all associated files with the plugin execution (edna xml input/output, 3rd party output files)
The base directory is the parent directory of the working directory.
Example: the working directory of a control plugin is the base directory of the plugins that it invokes,
i.e. the plugins working directories has the control plugin working directory as parent.
- defines the method that generates an executive summary (user-related output summary) that sub-classes should implement
"""
CONF_BASE_DIR_LABEL = "baseDirectory"
CONF_WORKING_DIR_LABEL = "workingDirectory"
CONF_TIME_OUT = "timeOut"
CONF_WRITE_XML_INPUT_OUTPUT = "writeXMLInputOutput"
CONF_WRITE_XML_OUTPUT = "writeXMLOutput"
CONF_WRITE_XML_INPUT = "writeXMLInput"
def __init__(self):
"""
Initializes plugin related attributes described above
"""
EDAction.__init__(self)
self.__xsPluginItem = None
self.__dictXSDataInputClass = {}
self.__dictXSDataInput = {}
self.__dictXSDataOutput = {}
self.__strDefaultInputDataKey = "defaultInputData"
self.__strDefaultOutputDataKey = "defaultOutputData"
self.__edSlotExportDataOutput = EDSlot()
self.__strBaseDirectory = None
self.__strWorkingDirectory = None
self.__strBaseName = None
self.__listExecutiveSummaryLines = []
self.__strExecutiveSummarySeparator = "-" * 80
self.__listErrorMessages = []
self.__listWarningMessages = []
self.__isRequiredToHaveConfiguration = False
self.__bWriteDataXMLInputOutput = True
self.__bWriteDataXMLOutput = True
self.__bWriteDataXMLInput = True
self.__strPluginId = "%s-%08i" % (self.getClassName(), self.getId())
self.strPathDataInput = None
self.strPathDataOutput = None
self.__bUseWarningInsteadOfError = False
self.__edConfiguration = EDConfigurationStatic()
def preProcess(self, _edObject=None):
"""
Writes xml data input in the working dir (if required)
Connects a slot for generating the executive summary after the plugin execution
Connects a slot for checking output data to the finally process
Initialize the base directory
Configures the plugin
Checks the input data
"""
EDAction.preProcess(self, _edObject)
self.DEBUG("EDPlugin.preProcess")
self.connectPostProcess(self.exportDataOutput)
if self.__bWriteDataXMLInputOutput:
if self.__bWriteDataXMLInput:
self.connectPreProcess(self.writeDataInput)
self.connectPostProcess(self.generateExecutiveSummary)
self.connectFinallyProcess(self.checkDataOutput)
if (self.__strBaseName is None):
self.setBaseName(self.createBaseName())
EDStatus.tellRunning(self.__strPluginId)
self.connectFinallyProcess(self.tellFinished)
self.checkParameters()
def tellFinished(self, _edObject=None):
"""
Tell EDStatus that the plugin has finished, either in success either in error
"""
if self.isFailure():
EDStatus.tellFailure(self.__strPluginId)
else:
EDStatus.tellSuccess(self.__strPluginId)
def checkDataOutput(self, _edObject=None):
"""
Checks if output data is available, if not issues a warning and sets an empty XSDataResult as output data
Writes xml data output in the working dir (if required)
"""
EDAction.finallyProcess(self, _edObject)
if self.__dictXSDataOutput == {}:
strWarningMessage = "Output data for plugin %s not set, using XSDataResult as output" % self.getPluginName(
)
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self.setDataOutput(XSDataResult())
if self.__bWriteDataXMLInputOutput:
if self.__bWriteDataXMLOutput:
self.writeDataOutput()
def synchronize(self):
"""
This method calls EDAction.synchronize and if a time-out occurs an error message
is added to the list of error messages.
"""
EDAction.synchronize(self)
if self.isTimeOut():
strErrorMessage = "Timeout when waiting for %s to terminate." % self.getClassName(
)
self.addErrorMessage(strErrorMessage)
def getConfig(self):
"""
Gets the Plugin Configuration as a dictionary
"""
# self.DEBUG("EDPlugin.getConfig")
return self.__edConfiguration.get(self.getPluginName(), {})
def setConfig(self, _dict, _bLocal=False):
"""
Receives a dictionary (Plugin Configuration) from the application.
"""
self.DEBUG("EDPlugin.setConfiguration")
if _bLocal:
self.__edConfiguration = EDConfiguration()
if _dict is not None:
self.__edConfiguration[self.getPluginName()] = _dict
else:
self.__edConfiguration[self.getPluginName()] = {}
config = property(getConfig, setConfig)
def configure(self):
"""
Should be overridden by the Final Plugin If needed
This method should set its proper members attributes from a Plugin configuration Object
"""
self.DEBUG("EDPlugin.configure : plugin name = %s, EDNA_SITE = %s" %
(self.getPluginName(), EDUtilsPath.EDNA_SITE))
# set Timeout if different from default one
if self.getTimeOut() == self.getDefaultTimeOut():
# Try to get time out from plugin configuration
iTimeOut = self.config.get(EDPlugin.CONF_TIME_OUT, None)
if iTimeOut is not None:
self.DEBUG(
"EDPlugin.configure: Setting time out to %d s from plugin configuration."
% iTimeOut)
self.setTimeOut(iTimeOut)
else:
self.DEBUG(
"EDPlugin.configure: timeout already set before plugin is configured."
)
# Base directory
strBaseDirectory = self.getBaseDirectory()
if (strBaseDirectory is None):
# Try to get base directory from plugin configuration
strBaseDirectory = self.config.get(EDPlugin.CONF_BASE_DIR_LABEL,
None)
if (strBaseDirectory is None):
# Try to get working directory from environment variable
strBaseDirectory = os.environ.get("EDNA_BASE_DIRECTORY")
if (strBaseDirectory is None):
self.DEBUG(
"EDPlugin.configure: Using current base directory as working directory."
)
strBaseDirectory = os.getcwd()
else:
self.DEBUG(
"EDPlugin.configure: Setting base directory from $EDNA_WORKING_DIRECTORY."
)
else:
if (strBaseDirectory == "."):
self.DEBUG(
"EDPlugin.configure: Using current base directory as working directory."
)
strBaseDirectory = os.getcwd()
else:
strBaseDirectory = os.path.abspath(strBaseDirectory)
self.DEBUG(
"EDPlugin.configure: Setting base directory from plugin configuration."
)
self.setBaseDirectory(strBaseDirectory)
else:
self.DEBUG(
"EDPlugin.configure: Base directory already set before plugin is configured."
)
# Working directory
strWorkingDirectory = self.getWorkingDirectory()
if (strWorkingDirectory is None):
# Try to get working directory from plugin configuration
strWorkingDirectory = self.config.get(
EDPlugin.CONF_WORKING_DIR_LABEL, None)
if (strWorkingDirectory is not None):
self.DEBUG(
"EDPlugin.configure: Setting working directory from plugin configuration."
)
else:
self.DEBUG(
"EDPlugin.configure: Setting working directory as base directory + base name."
)
strWorkingDirectory = os.path.join(self.getBaseDirectory(),
self.getBaseName())
self.setWorkingDirectory(strWorkingDirectory)
else:
self.DEBUG(
"EDPlugin.configure: Working directory already set before plugin is configured."
)
#
self.__bWriteDataXMLInputOutput = bool(
self.config.get(self.CONF_WRITE_XML_INPUT_OUTPUT, True))
self.__bWriteDataXMLOutput = bool(
self.config.get(self.CONF_WRITE_XML_OUTPUT, True))
self.__bWriteDataXMLInput = bool(
self.config.get(self.CONF_WRITE_XML_INPUT, True))
def execute(self, _edObject=None):
# Configure the plugin before starting it's thread
self.configure()
EDAction.execute(self, _edObject)
def checkParameters(self):
"""
Should be overridden by the Final Plugin If needed
This method should check that the data input are consistent
"""
self.DEBUG("EDPlugin.checkParameters")
def setXSDataInputClass(self, _xsDataInputClass, _strDataInputKey=None):
"""
This method should be called in the constructor of the derived plugins
in order to set the XSData type of the input data, e.g. XSDataInputXXX
"""
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInputClass.keys()):
strErrorMessage = "ERROR: " + self.getPluginName(
) + ".setXSDataInputClass, Data Input Class already defined for key: " + strDataInputKey
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
self.__dictXSDataInputClass[strDataInputKey] = _xsDataInputClass
def getXSDataInputClass(self, _strDataInputKey=None):
"""
Returns the XSData type of the input data.
"""
pyXSDataInputClass = None
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInputClass.keys()):
pyXSDataInputClass = self.__dictXSDataInputClass[strDataInputKey]
return pyXSDataInputClass
def setDataInput(self, _oDataInput, _strDataInputKey=None):
"""
Sets the plugin input data.
_oDataInput could be either an String XML or an XSData object.
The input data is stored in a dictionary with the key _strDataInputKey.
If the key is not provided a default key is used.
If not data input class is defined for the key an exception is raised.
If the key is not the default key, the data object is added to a list which
might contain already stored object(s).
If _oDataInput is None the list corresponding to a keyword is deleted.
"""
self.DEBUG("EDPlugin.setDataInput")
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
# Allow for None input
if (_oDataInput is None):
self.DEBUG("EDPlugin.setDataInput: Data input is None")
self.__dictXSDataInput[strDataInputKey] = []
elif (self.getXSDataInputClass(strDataInputKey) is None):
strErrorMessage = "ERROR: " + self.getPluginName(
) + ".setDataInput, Data Input Class not defined for key: " + strDataInputKey
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
# Check the type
xsDataInput = None
if isinstance(_oDataInput, (str, unicode)):
self.DEBUG("EDPlugin.setDataInput: Input Data is string ")
xsDataInput = self.getXSDataInputClass(
strDataInputKey).parseString(_oDataInput)
elif (isinstance(_oDataInput,
self.getXSDataInputClass(strDataInputKey))):
self.DEBUG("EDPlugin.setDataInput: Input Data is of type " +
str(_oDataInput.__class__))
xsDataInput = _oDataInput
else:
strErrorMessage = "ERROR: %s.setDataInput, wrong data type %r for data input key: %s, expected XML string or %r" % \
(self.getPluginName(), _oDataInput.__class__, strDataInputKey, self.getXSDataInputClass(strDataInputKey))
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
# Add the object to a list if its key is not the default key
if (strDataInputKey != self.__strDefaultInputDataKey):
# Check if there's already a list stored
if (not strDataInputKey in self.__dictXSDataInput.keys()):
self.__dictXSDataInput[strDataInputKey] = []
self.__dictXSDataInput[strDataInputKey].append(xsDataInput)
else:
self.__dictXSDataInput[strDataInputKey] = xsDataInput
def hasDataInput(self, _strDataInputKey=None):
"""
Returns True if the plugin has Input Data for a particular key.
If the key is not provided a default key is used.
"""
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInput.keys()):
return True
else:
return False
def getDataInput(self, _strDataInputKey=None):
"""
Returns the Plugin Input Data for a particular key.
If the key is not provided a default key is used.
"""
oValue = None
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInput.keys()):
oValue = self.__dictXSDataInput[strDataInputKey]
else:
strErrorMessage = self.getPluginName(
) + ".getDataInput, no input data defined for key: " + strDataInputKey
self.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
return oValue
def delDataInput(self, _strDataInputKey=None):
"""
Deletes the data input for a particular key.
If the key is not provided a default key is used.
"""
strDataInputKey = _strDataInputKey
if (strDataInputKey is None):
strDataInputKey = self.__strDefaultInputDataKey
if (strDataInputKey in self.__dictXSDataInput.keys()):
self.__dictXSDataInput[strDataInputKey] = None
else:
strErrorMessage = self.getPluginName(
) + ".delDataInput, no input data defined for key: " + strDataInputKey
self.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
# Property for dataInput
dataInput = property(getDataInput, setDataInput, delDataInput,
"Property for dataInput")
def setDataOutput(self, _xsDataOutput, _strDataOutputKey=None):
"""
Sets the plugin output data for a particular key.
If the key is not provided a default key is used.
If the key is already defined in the dictionary, the corresponding
data object is added to a list which contains the already stored object(s).
"""
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self.__strDefaultOutputDataKey
# Add the object to a list if its key not the default key
if (strDataOutputKey == self.__strDefaultOutputDataKey):
self.__dictXSDataOutput[strDataOutputKey] = _xsDataOutput
else:
# Check if the _xsDataoutput object is already a list
if (type(_xsDataOutput) == list):
self.__dictXSDataOutput[strDataOutputKey] = _xsDataOutput
else:
# Check if the stored object contains already a list
if (not strDataOutputKey in self.__dictXSDataOutput.keys()):
self.__dictXSDataOutput[strDataOutputKey] = []
self.__dictXSDataOutput[strDataOutputKey].append(_xsDataOutput)
def getDataOutput(self, _strDataOutputKey=None):
"""
Returns the Plugin Output Data
"""
oValue = None
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self.__strDefaultOutputDataKey
if (strDataOutputKey in self.__dictXSDataOutput.keys()):
oValue = self.__dictXSDataOutput[strDataOutputKey]
return oValue
def hasDataOutput(self, _strDataOutputKey=None):
"""
Returns True if the plugin has the specified Output Data
"""
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self.__strDefaultOutputDataKey
if (strDataOutputKey in self.__dictXSDataOutput.keys()):
return True
else:
return False
def delDataOutput(self, _strDataOutputKey=None):
"""
Deletes the data output for a particular key.
If the key is not provided a default key is used.
"""
strDataOutputKey = _strDataOutputKey
if (strDataOutputKey is None):
strDataOutputKey = self.__strDefaultOutputDataKey
if (strDataOutputKey in self.__dictXSDataOutput.keys()):
self.__dictXSDataOutput[strDataOutputKey] = None
else:
strErrorMessage = self.getPluginName(
) + ".delDataOutput, no output data defined for key: " + _strDataOutputKey
self.warning(strErrorMessage)
self.addWarningMessage(strErrorMessage)
# Property for dataOutput
dataOutput = property(getDataOutput, setDataOutput, delDataOutput,
"Property for dataOutput")
def exportDataOutput(self, _edPlugin=None):
"""
Deprecated
Exports the Plugin Output Data to slot
"""
self.DEBUG("EDPlugin.exportDataOutput")
self.__edSlotExportDataOutput.call(self.__dictXSDataOutput)
def connectExportDataOutput(self, _oMethod):
"""
Deprecated
"""
self.synchronizeOn()
if (_oMethod != None):
self.__edSlotExportDataOutput.connect(_oMethod)
self.synchronizeOff()
def generateExecutiveSummary(self, _edPlugin):
"""
This method, which should be implemented by sub-classes, generates an executive summary (user-related output summary).
"""
self.DEBUG("EDPlugin.generateExecutiveSummary")
def addErrorMessage(self, _strErrorMessage):
"""
Adds an error message to the error messages list
"""
self.__listErrorMessages.append(_strErrorMessage)
def getListOfErrorMessages(self):
"""
Returns the error messages list
"""
return self.__listErrorMessages
def addWarningMessage(self, _strWarningMessage):
"""
Adds a warning message to the warning messages list
"""
self.DEBUG("EDPlugin.addWarningMessage : " + _strWarningMessage)
self.__listWarningMessages.append(_strWarningMessage)
def getListOfWarningMessages(self):
"""
Returns the warning messages list
"""
return self.__listWarningMessages
def writeDataInput(self, _edObject=None):
"""
Writes the input data object(s) into a working dir xml file
"""
self.DEBUG("EDPlugin.writeDataInput")
strBasename = os.path.join(
self.getWorkingDirectory(),
self.compactPluginName(self.getPluginName()))
for strKey in self.__dictXSDataInput.keys():
if (strKey == self.__strDefaultInputDataKey): # "Old" style
xsDataInput = self.__dictXSDataInput[
self.__strDefaultInputDataKey]
self.strPathDataInput = strBasename + "_dataInput.xml"
EDUtilsFile.writeFile(self.strPathDataInput,
xsDataInput.marshal())
else: # We have a list of objects
listXSDataInput = self.__dictXSDataInput[strKey]
for iIndex, xsDataInput in enumerate(listXSDataInput):
strPathDataInput = "%s_%s_%d_dataInput.xml" % (
strBasename, strKey, iIndex)
EDUtilsFile.writeFile(strPathDataInput,
xsDataInput.marshal())
def writeDataOutput(self, _edObject=None):
"""
Writes the output data object(s) into a working dir xml file
"""
self.DEBUG("EDPlugin.writeDataOutput")
for strKey in self.__dictXSDataOutput.keys():
if (strKey == self.__strDefaultOutputDataKey): # "Old" style
xsDataOutput = self.__dictXSDataOutput[
self.__strDefaultOutputDataKey]
if (xsDataOutput is not None):
self.strPathDataOutput = os.path.join(
self.getWorkingDirectory(),
self.compactPluginName(self.getPluginName()) +
"_dataOutput.xml")
EDUtilsFile.writeFile(self.strPathDataOutput,
xsDataOutput.marshal())
else:
listXSDataOutput = self.__dictXSDataOutput[strKey]
for iIndex, xsDataOutput in enumerate(listXSDataOutput):
if (xsDataOutput is not None):
strPathDataOutput = os.path.join(
self.getWorkingDirectory(),
self.compactPluginName(self.getPluginName()) +
"_" + strKey + "_%d_dataOutput.xml" % iIndex)
EDUtilsFile.writeFile(strPathDataOutput,
xsDataOutput.marshal())
def getBaseName(self):
"""
Returns the plugin base name
"""
if (self.__strBaseName is None):
self.__strBaseName = self.createBaseName()
return self.__strBaseName
def setBaseName(self, _strBaseName):
"""
Sets the plugin base name
"""
self.__strBaseName = self.compactPluginName(_strBaseName)
self.setName(self.__strBaseName)
# Create the directory baseDirectory/baseName which will be used as working directory
strWorkingDirPath = os.path.join(self.getBaseDirectory(),
self.__strBaseName)
if not os.path.isdir(strWorkingDirPath):
os.mkdir(strWorkingDirPath)
self.setWorkingDirectory(strWorkingDirPath)
def createBaseName(self):
"""
Generates the plugin base name: (<prefix>-<object ID>)
"""
# First try to use global instance ID from EDObject
strBaseName = "%s-%08d" % (self.compactPluginName(
self.getPluginName()), self.getId())
strBaseDir = os.path.join(self.getBaseDirectory(), strBaseName)
# Try to create the directory...
try:
os.mkdir(strBaseDir)
except Exception as strErrorDetail:
self.error(
"EDPlugin.createBaseName: Could not create base directory %s because of %s"
% (strBaseDir, strErrorDetail))
self.warning(
"EDPlugin.createBaseName: Trying to create alternative base directory..."
)
self.writeErrorTrace()
strTempDir = tempfile.mkdtemp(prefix=strBaseName,
dir=self.getBaseDirectory())
os.chmod(
strTempDir, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR
| stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)
strBaseName = os.path.split(strTempDir)[1]
strBaseDir = os.path.join(self.getBaseDirectory(), strBaseName)
self.warning(
"EDPlugin.createBaseName: Alternative base directory created: %s"
% strBaseDir)
self.DEBUG("EDPlugin.createBaseName : Directory created = " +
strBaseDir)
return strBaseName
def compactPluginName(self, _pluginName):
"""
The prefix is constructed from the plugin name with the following renaming:
EDPlugin -> ""
EDPluginExec -> ""
EDPluginControl -> "Control"
"""
strCompactName = _pluginName
if (strCompactName.startswith("EDPluginExec")):
strCompactName = strCompactName[12:]
elif (strCompactName.startswith("EDPluginControl")):
strCompactName = strCompactName[8:]
elif (strCompactName.startswith("EDPlugin")):
strCompactName = strCompactName[8:]
return strCompactName
def setBaseDirectory(self, _strBaseDirectory):
"""
Sets the plugin base directory
"""
self.DEBUG("EDPlugin.setBaseDirectory : " + _strBaseDirectory)
if (not os.path.isdir(_strBaseDirectory)):
self.DEBUG(
"EDPlugin.setBaseDirectory: base directory %s does dot yet exist! Creating it."
% _strBaseDirectory)
os.mkdir(_strBaseDirectory)
self.__strBaseDirectory = _strBaseDirectory
def getBaseDirectory(self):
"""
Returns the plugin base directory
"""
self.DEBUG("EDPlugin.getBaseDirectory : %s" % self.__strBaseDirectory)
if (self.__strBaseDirectory is None):
self.__strBaseDirectory = os.getcwd()
return self.__strBaseDirectory
def setWorkingDirectory(self, _strWorkingDirectory):
"""
Sets the plugin working directory
"""
self.DEBUG("EDPlugin.setWorkingDirectory : " + _strWorkingDirectory)
self.__strWorkingDirectory = _strWorkingDirectory
if not os.path.isdir(_strWorkingDirectory):
self.DEBUG(
"EDPlugin.setWorkingDirectory, creating working directory %s."
% _strWorkingDirectory)
os.mkdir(self.__strWorkingDirectory)
def getWorkingDirectory(self):
"""
Returns the plugin base directory
"""
self.DEBUG("EDPlugin.getWorkingDirectory : %s" %
self.__strWorkingDirectory)
returnValue = None
if (self.__strWorkingDirectory is not None):
returnValue = self.__strWorkingDirectory
return returnValue
def checkMandatoryParameters(self, _xsData, _strParamName):
"""
Checks that a mandatory parameter exists in the data
If not, an error message is added in the list and the plugin fails
"""
if _xsData is None or (hasattr(_xsData, '__len__')
and len(_xsData) == 0):
strErrorMessage = "%s: input parameter is missing: %s" % (
self.getPluginName(), _strParamName)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
def checkImportantParameters(self, _xsData, _strParamName):
"""
Checks that a specific parameter exists in the data
If not, a warning message is added in the list
"""
if (_xsData == None):
strWarningMessage = "%s: input parameter is missing: %s" % (
self.getPluginName(), _strParamName)
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
def addExecutiveSummaryLine(self, _strExecutiveSummaryLine):
"""
Add a line to the executive summary string.
"""
self.DEBUG("EDPlugin.addExecutiveSummaryLine : %r" %
_strExecutiveSummaryLine)
strExecutiveSummaryLine = _strExecutiveSummaryLine
if (not strExecutiveSummaryLine == ""):
if (strExecutiveSummaryLine[-1] == "\n"):
strExecutiveSummaryLine = strExecutiveSummaryLine[:-1]
self.__listExecutiveSummaryLines.append(strExecutiveSummaryLine)
def addExecutiveSummarySeparator(self, _strSeparator=None):
"""
Adds a separator to split the executive summary into different parts
Default is a dotted line
"""
strSeparator = _strSeparator
if (strSeparator is None):
strSeparator = self.__strExecutiveSummarySeparator
# Check that the last line doesn't already contain a separator
if self.__listExecutiveSummaryLines != []:
if self.__listExecutiveSummaryLines[-1] != strSeparator:
self.addExecutiveSummaryLine(strSeparator)
else:
self.addExecutiveSummaryLine(strSeparator)
def getListExecutiveSummaryLines(self):
"""
Returns the executive summary (list of text lines)
"""
return self.__listExecutiveSummaryLines
def verboseScreenExecutiveSummary(self):
"""
Prints the executive summary on the screen
"""
for line in self.getListExecutiveSummaryLines():
self.screen(line)
def verboseDebug(self, _strMessage):
self.DEBUG(self.getPluginName() + " : " + _strMessage)
def getPluginName(self):
return self.getClassName()
def getListOfDataInputKeys(self):
return self.__dictXSDataInput.keys()
def getListOfDataOutputKeys(self):
return self.__dictXSDataOutput.keys()
def getDefaultInputDataKey(self):
return self.__strDefaultInputDataKey
def getDefaultOutputDataKey(self):
return self.__strDefaultOutputDataKey
def getExecutiveSummarySeparator(self):
return self.__strExecutiveSummarySeparator
def isRequiredToHaveConfiguration(self):
"""
If the return value from this method is true, the plugin
is required to have a configuration in order to be executed in a
plugin execution test case.
@return: RequiredToHaveConfiguration
@rtype: boolean
"""
return self.__isRequiredToHaveConfiguration
def setRequiredToHaveConfiguration(self, _bValue=True):
"""
Sets or unsets the plugin to be required to have a configuration
for execution in a plugin execution test case.
plugin execution test case.
@param _bValue: RequiredToHaveConfiguration
@type: boolean
"""
self.__isRequiredToHaveConfiguration = _bValue
def setWriteXMLInputOutput(self, _bValue=True):
"""
Sets or unsets the plugin to write XML input and output files.
@param _bValue: WriteDataXMLInputOutput
@type: boolean
"""
self.__bWriteDataXMLInputOutput = _bValue
def setWriteXMLInput(self, _bValue=True):
"""
Sets or unsets the plugin to write XML input files.
@param _bValue: WriteDataXMLInput
@type: boolean
"""
self.__bWriteDataXMLInput = _bValue
def setWriteXMLOutput(self, _bValue=True):
"""
Sets or unsets the plugin to write XML output files.
@param _bValue: WriteDataXMLOutput
@type: boolean
"""
self.__bWriteDataXMLOutput = _bValue
def setUseWarningInsteadOfError(self, _bValue=True):
"""
Sets or unsets the plugin to use warning messages also for error messages.
@param _bValue: UseWarningInsteadOfError
@type: boolean
"""
self.__bUseWarningInsteadOfError = _bValue
def error(self, _strErrorMessage):
"""
Overloaded from EDLogging. If self.__bUseWarningInsteadOfError is True
a warning message is issued instead of an error message.
"""
if self.__bUseWarningInsteadOfError:
self.warning(_strErrorMessage)
else:
EDAction.error(self, _strErrorMessage)
def ERROR(self, _strErrorMessage):
"""
Uses the overloaded self.error method above.
"""
self.error(_strErrorMessage)
def testSetDataModelInput(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
xsDataStrategy = XSDataInputStrategy()
# Beam
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setWavelength(XSDataWavelength(2.41))
xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsBeam.setExposureTime(XSDataTime(1))
xsExperimentalCondition.setBeam(xsBeam)
# Detector and Exposure Time
xsDataDetector = XSDataDetector()
xsDataDetector.setType(XSDataString("q210-2x"))
xsExperimentalCondition.setDetector(xsDataDetector)
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setRotationAxis(XSDataString("phi"))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)
# Best Files
bestFileContentDat = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.dat"))
xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.par"))
xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile1.hkl"))
xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))
# Crystal
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataDouble(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))
xsDataStrategy.setCrystalRefined(xsDataCrystal)
xsDataStrategy.setSample(xsDataSampleCrystalMM)
xsDataStrategy.exportToFile(self.strObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile (self.strReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile (self.strObtainedInputFile)
xsDataInputExpected = XSDataInputStrategy.parseString(pyStrExpectedInput)
xsDataInputObtained = XSDataInputStrategy.parseString(pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
def testSetDataModelInput(self):
edPluginBest = self.createPlugin()
edConfigurationGood01 = EDConfiguration(
os.path.join(self.strDataPath, "XSConfiguration.xml"))
dictItemGood01 = edConfigurationGood01.get(self.getPluginName())
edPluginBest.setConfig(dictItemGood01, _bLocal=True)
edPluginBest.setScriptExecutable("cat")
edPluginBest.configure()
from XSDataBestv1_3 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 XSDataAngularSpeed
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(XSDataAngularSpeed(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(
os.path.join(self.strDataPath, "bestfile.dat"))
xsDataInputBest.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.par"))
xsDataInputBest.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile1.hkl"))
xsDataInputBest.addBestFileContentHKL(XSDataString(bestFileContentHKL))
xsDataInputBest.exportToFile(self.obtainedInputFile)
pyStrExpectedInput = self.readAndParseFile(self.referenceInputFile)
pyStrObtainedInput = self.readAndParseFile(self.obtainedInputFile)
xsDataInputExpected = XSDataInputBest.parseString(pyStrExpectedInput)
xsDataInputObtained = XSDataInputBest.parseString(pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
EDUtilsFile.deleteFile(self.obtainedInputFile)
self.cleanUp(edPluginBest)
