def testCheckParameters(self):
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataResultCharacterisation = XSDataResultCharacterisation()
xsDataInputControlISPyB.setCharacterisationResult(xsDataResultCharacterisation)
edPluginControlISPyB = self.createPlugin()
edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
edPluginControlISPyB.checkParameters()
def testCheckParameters(self):
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataResultCharacterisation = XSDataResultCharacterisation
xsDataInputControlISPyB.setCharacterisationResult(
xsDataResultCharacterisation)
edPluginControlISPyB = self.createPlugin()
edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
edPluginControlISPyB.checkParameters()
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath,
strReferenceInputControlISPyBFile)
strXMLIndexingInput = self.readAndParseFile(strPath)
from XSDataMXv1 import XSDataInputControlISPyB
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(
strXMLIndexingInput)
from EDHandlerXSDataISPyBv1_1 import EDHandlerXSDataISPyBv1_1
xsDataInputISPyB = EDHandlerXSDataISPyBv1_1.generateXSDataInputISPyB(
xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath,
strReferenceInputISPyBFile)
strXMLInputISPyBReference = self.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataInputISPyB
xsDataInputISPyBReference = XSDataInputISPyB.parseString(
strXMLInputISPyBReference)
# Remove the time strings since they otherwise make the test fail
xsDataInputISPyBReference.getScreening().setTimeStamp(None)
xsDataInputISPyB.getScreening().setTimeStamp(None)
EDAssert.equal(xsDataInputISPyBReference.marshal(),
xsDataInputISPyB.marshal())
def testGetBestWilsonPlotPath(self):
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataCharacterisationResult = xsDataInputControlISPyB.characterisationResult
strPath = EDHandlerXSDataISPyBv1_4.getBestWilsonPlotPath(xsDataCharacterisationResult)
EDAssert.equal(True, strPath.endswith("B.jpg"), "Wilson plot path extracted from characterisation results")
def storeResultsInISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev1_3.storeResultsInISPyB")
if (self.edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(self.edPluginControlCharacterisation.getDataOutput())
if (not self.iDataCollectionId is None):
dataCollectionGroupId = self.getDataCollectionGroupId(self.iDataCollectionId)
xsDataInputControlISPyB.setDataCollectionGroupId(XSDataInteger(dataCollectionGroupId))
if (not self.strShortComments is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strShortComments), "shortComments")
if (not self.strComments is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strComments), "comments")
if (not self.strStatusMessage is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strStatusMessage), "statusMessage")
self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.edPluginControlISPyB.executeSynchronous()
self.checkDozorScores(self.edPluginControlCharacterisation.getDataOutput())
def storeResultsInISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev1_3.storeResultsInISPyB")
if (self.edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(
self.edPluginControlCharacterisation.getDataOutput())
if (not self.iDataCollectionId is None):
dataCollectionGroupId = self.getDataCollectionGroupId(
self.iDataCollectionId)
xsDataInputControlISPyB.setDataCollectionGroupId(
XSDataInteger(dataCollectionGroupId))
if (not self.strShortComments is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strShortComments), "shortComments")
if (not self.strComments is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strComments), "comments")
if (not self.strStatusMessage is None):
self.edPluginControlISPyB.setDataInput(
XSDataString(self.strStatusMessage), "statusMessage")
self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.edPluginControlISPyB.executeSynchronous()
self.checkDozorScores(
self.edPluginControlCharacterisation.getDataOutput())
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataInputISPyB = EDHandlerXSDataISPyBv1_4.generateXSDataInputISPyBStoreScreening(xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = EDUtilsFile.readFileAndParseVariables(strReferencePath, self.dictReplace)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_4")
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
xsDataInputISPyB = EDHandlerXSDataISPyBv1_3.generateXSDataInputISPyBStoreScreening(xsDataInputControlISPyB)
print xsDataInputISPyB.marshal()
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = EDUtilsFile.readFileAndParseVariables(strReferencePath, self.dictReplace)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_3")
def testGetBestWilsonPlotPath(self):
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(
self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath,
strReferenceInputControlISPyBFile)
strXMLIndexingInput = EDUtilsFile.readFileAndParseVariables(
strPath, self.dictReplace)
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(
strXMLIndexingInput)
xsDataCharacterisationResult = xsDataInputControlISPyB.characterisationResult
strPath = EDHandlerXSDataISPyBv1_4.getBestWilsonPlotPath(
xsDataCharacterisationResult)
EDAssert.equal(
True, strPath.endswith("B.jpg"),
"Wilson plot path extracted from characterisation results")
def storeResultsInISPyB(self, _edPlugin=None):
self.DEBUG("EDPluginControlInterfacev2_0.storeResultsInISPyB")
if (self.edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(self.edPluginControlCharacterisation.getDataOutput().getMxv1ResultCharacterisation())
if (not self.iDataCollectionId is None):
xsDataInputControlISPyB.setDataCollectionId(XSDataInteger(self.iDataCollectionId))
if (not self.strShortComments is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strShortComments), "shortComments")
if (not self.strComments is None):
self.edPluginControlISPyB.setDataInput(XSDataString(self.strComments), "comments")
self.edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.edPluginControlISPyB.executeSynchronous()
def testGenerateXSDataInputISPyB(self):
"""
This method is testing the generation of the XSDataInputISPyB object given a XSDataIndexingInput object.
"""
strReferenceInputControlISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputControlISPyB_reference.xml")
strPath = os.path.join(self.strDataPath, strReferenceInputControlISPyBFile)
strXMLIndexingInput = self.readAndParseFile(strPath)
from XSDataMXv1 import XSDataInputControlISPyB
xsDataInputControlISPyB = XSDataInputControlISPyB.parseString(strXMLIndexingInput)
from EDHandlerXSDataISPyBv1_1 import EDHandlerXSDataISPyBv1_1
xsDataInputISPyB = EDHandlerXSDataISPyBv1_1.generateXSDataInputISPyB(xsDataInputControlISPyB)
strReferenceInputISPyBFile = EDUtilsPath.mergePath(self.strDataPath, "XSDataInputISPyB_reference.xml")
strReferencePath = os.path.join(self.strDataPath, strReferenceInputISPyBFile)
strXMLInputISPyBReference = self.readAndParseFile(strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataISPyBv1_1")
from XSDataISPyBv1_1 import XSDataInputISPyB
xsDataInputISPyBReference = XSDataInputISPyB.parseString(strXMLInputISPyBReference)
# Remove the time strings since they otherwise make the test fail
xsDataInputISPyBReference.getScreening().setTimeStamp(None)
xsDataInputISPyB.getScreening().setTimeStamp(None)
EDAssert.equal(xsDataInputISPyBReference.marshal(), xsDataInputISPyB.marshal())
def testCheckParameters(self):
xsDataInput = XSDataInputControlISPyB()
edPluginExecISPyB = self.createPlugin()
edPluginExecISPyB.setDataInput(xsDataInput)
edPluginExecISPyB.checkParameters()
class EDPluginControlInterfaceToMXCuBEv1_2(EDPluginControl):
"""
This is the plugin interface to launch the MXv1 characterisation from an MXCuBE gui.
It is for the moment a wrapper for the EDPluginControlCCP4iv1_1 plugin, which also
runs the ISPyB control plugin if a data collection id is available.
"""
__EDNA_CONTACT_EMAIL = "contactEmail"
__EDNA_EMAIL_SENDER = "emailSender"
def __init__ (self):
"""
Initialisation of EDPluginControlInterfaceToMXCuBEv1_2:
- Input data type class : XSDataInputMXCuBE
- Name of default characterisation plugin : EDPluginControlCharacterisationv1_1
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputMXCuBE)
self.__strPluginControlCCP4i = "EDPluginControlCCP4iv1_1"
self.__edPluginControlCCP4i = None
self.__strPluginControlISPyB = "EDPluginControlISPyBv1_0"
self.__edPluginControlISPyB = None
self.__xsDataResultMXCuBE = None
self.__xsDataIntegerDataCollectionId = None
self.__strPluginExecOutputHTMLName = "EDPluginExecOutputHTMLv1_0"
self.__edPluginExecOutputHTML = None
self.__strEDNAContactEmail = None
self.__strEDNAEmailSender = "*****@*****.**"
def checkParameters(self):
"""
Checks the mandatory input parameters :
- dataSet
- outputFileDirectory
"""
self.verboseDebug("EDPluginControlInterfaceToMXCuBEv1_2.checkParameters")
self.checkMandatoryParameters(self.getDataInput(), "Data Input is None")
self.checkMandatoryParameters(self.getDataInput().getDataSet(), "dataSet")
#self.checkMandatoryParameters( self.getDataInput().getOutputFileDirectory(), "outputFileDirectory" )
def configure(self):
EDPluginControl.configure(self)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.configure")
xsPluginItem = self.getConfiguration()
if xsPluginItem == None:
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.configure: No plugin item defined.")
else:
self.__strEDNAContactEmail = EDConfiguration.getStringParamValue(xsPluginItem, EDPluginControlInterfaceToMXCuBEv1_2.__EDNA_CONTACT_EMAIL)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.configure: EDNAContactEmail = %s" % self.__strEDNAContactEmail)
strEDNAEmailSender = EDConfiguration.getStringParamValue(xsPluginItem, self.__EDNA_EMAIL_SENDER)
if strEDNAEmailSender:
self.__strEDNAEmailSender = strEDNAEmailSender
def preProcess(self, _edPlugin=None):
"""
This method prepares the input for the CCP4i plugin and loads it.
"""
EDPluginControl.preProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.preProcess...")
EDFactoryPluginStatic.loadModule("XSDataCCP4iv1_1")
from XSDataCCP4iv1_1 import XSDataInputCCP4i
xsDataInputCCP4i = XSDataInputCCP4i()
xsDataInputMXCuBE = self.getDataInput()
xsDataInputCCP4i.setDataSet(xsDataInputMXCuBE.getDataSet())
#xsDataInputCCP4i.setDataFile( xsDataInputMXCuBE.getDataFile() )
xsDataInputCCP4i.setExperimentalCondition(xsDataInputMXCuBE.getExperimentalCondition())
xsDataInputCCP4i.setDiffractionPlan(xsDataInputMXCuBE.getDiffractionPlan())
xsDataInputCCP4i.setSample(xsDataInputMXCuBE.getSample())
self.__edPluginControlCCP4i = self.loadPlugin(self.__strPluginControlCCP4i, "CCP4i")
self.__edPluginControlCCP4i.setDataInput(xsDataInputCCP4i)
self.__xsDataIntegerDataCollectionId = xsDataInputMXCuBE.getDataCollectionId()
if (self.__xsDataIntegerDataCollectionId is not None):
self.__edPluginControlISPyB = self.loadPlugin(self.__strPluginControlISPyB, "ISPyB")
self.__edPluginExecOutputHTML = self.loadPlugin(self.__strPluginExecOutputHTMLName, "OutputHTML")
def process(self, _edPlugin=None):
EDPluginControl.process(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.process...")
if self.__edPluginControlCCP4i is not None:
self.connectProcess(self.__edPluginControlCCP4i.executeSynchronous)
self.__edPluginControlCCP4i.connectSUCCESS(self.doSuccessActionCCP4i)
self.__edPluginControlCCP4i.connectFAILURE(self.doFailureActionCCP4i)
if self.__edPluginControlISPyB is not None:
self.__edPluginControlISPyB.connectSUCCESS(self.doSuccessActionISPyB)
self.__edPluginControlISPyB.connectFAILURE(self.doFailureActionISPyB)
def postProcess(self, _edPlugin=None):
EDPluginControl.postProcess(self, _edPlugin)
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.postProcess...")
self.setDataOutput(self.__xsDataResultMXCuBE)
def doSuccessActionCCP4i(self, _edPlugin=None):
EDVerbose.DEBUG("EDPluginControlInterfaceToMXCuBEv1_2.doSuccessActionCCP4i...")
self.retrieveSuccessMessages(self.__edPluginControlCCP4i, "EDPluginControlInterfaceToMXCuBEv1_2.doSuccessActionCCP4i")
# Retrieve the results from the CCP4 plugin execution
xsDataResultCCP4i = self.__edPluginControlCCP4i.getDataOutput()
self.__xsDataResultMXCuBE = XSDataResultMXCuBE()
xsDataStringListOfOutputFiles = xsDataResultCCP4i.getListOfOutputFiles()
self.__xsDataResultMXCuBE.setListOfOutputFiles(xsDataStringListOfOutputFiles)
# Retrieve the characterisation output object
xsDataResultCharacterisation = self.getXSDataResultCharacterisation(xsDataStringListOfOutputFiles.getValue())
# For the moment, create "DNA" style output directory
strPathToDNAFileDirectory = self.createDNAFileDirectoryPath(xsDataResultCharacterisation)
xsDataDictionaryLogFile = None
if (self.createDNAFileDirectory(strPathToDNAFileDirectory)):
xsDataDictionaryLogFile = self.createOutputFileDictionary(xsDataStringListOfOutputFiles, xsDataResultCharacterisation, strPathToDNAFileDirectory)
strPyArchPathToDNAFileDirectory = self.createPyArchDNAFilePath(strPathToDNAFileDirectory)
if (self.createDNAFileDirectory(strPyArchPathToDNAFileDirectory)):
xsDataDictionaryLogFile = self.createOutputFileDictionary(xsDataStringListOfOutputFiles, xsDataResultCharacterisation, strPyArchPathToDNAFileDirectory)
self.__xsDataResultMXCuBE.setOutputFileDictionary(xsDataDictionaryLogFile)
# Send success email message (MXSUP-183):
strSubject = "%s : SUCCESS!" % EDUtilsPath.getEdnaSite()
strMessage = "Success!"
if xsDataDictionaryLogFile != None:
for xsDataKeyValuePair in xsDataDictionaryLogFile.getKeyValuePair():
strKey = xsDataKeyValuePair.getKey().getValue()
if strKey == "executiveSummary":
strPathToExecutiveSummary = xsDataKeyValuePair.getValue().getValue()
strMessage = EDUtilsFile.readFile(strPathToExecutiveSummary)
self.sendEmail(strSubject, strMessage)
# Fix for bug EDNA-55 : If burning strategy EDNA2html shouldn't be run
bRunExecOutputHTML = True
xsDataInputMXCuBE = self.getDataInput()
xsDataDiffractionPlan = xsDataInputMXCuBE.getDiffractionPlan()
if xsDataDiffractionPlan.getStrategyOption() is not None:
strStrategyOption = xsDataDiffractionPlan.getStrategyOption().getValue()
if strStrategyOption.find("-DamPar") != -1:
bRunExecOutputHTML = False
if (self.__edPluginExecOutputHTML is not None) and bRunExecOutputHTML:
self.__edPluginExecOutputHTML.executeSynchronous()
if not self.__edPluginExecOutputHTML.isFailure() and self.__edPluginExecOutputHTML.hasDataOutput("htmlFile"):
strPathToHTMLFile = self.__edPluginExecOutputHTML.getDataOutput("htmlFile")[0].getPath().getValue()
strPathToHTMLDir = self.__edPluginExecOutputHTML.getDataOutput("htmlDir")[0].getPath().getValue()
strPathToDNAIndexDirectory = os.path.join(strPathToDNAFileDirectory, "index")
if os.path.exists(strPathToHTMLFile):
try:
os.mkdir(strPathToDNAIndexDirectory)
shutil.copy(strPathToHTMLFile, os.path.join(strPathToDNAIndexDirectory, "index.html"))
shutil.copytree(strPathToHTMLDir, os.path.join(strPathToDNAIndexDirectory, os.path.basename(strPathToHTMLDir)))
if strPyArchPathToDNAFileDirectory is not None:
strPathToPyArchIndexDirectory = os.path.join(strPyArchPathToDNAFileDirectory, "index")
os.mkdir(strPathToPyArchIndexDirectory)
shutil.copy(strPathToHTMLFile, os.path.join(strPathToPyArchIndexDirectory, "index.html"))
shutil.copytree(strPathToHTMLDir, os.path.join(strPathToPyArchIndexDirectory, os.path.basename(strPathToHTMLDir)))
except Exception, e:
EDVerbose.DEBUG("Exception caught: %r" % e)
if (self.__edPluginControlISPyB is not None):
# Execute the ISPyB control plugin
xsDataInputControlISPyB = XSDataInputControlISPyB()
xsDataInputControlISPyB.setCharacterisationResult(xsDataResultCharacterisation)
xsDataInputControlISPyB.setDataCollectionId(self.__xsDataIntegerDataCollectionId)
self.__edPluginControlISPyB.setDataInput(xsDataInputControlISPyB)
self.__edPluginControlISPyB.executeSynchronous()
