def testExecute(self):
"""
"""
self.run()
# Checks that there are no error messages
plugin = self.getPlugin()
# Checks the expected result
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
# strObtainedOutput = plugin.getDataOutput().marshal() # EDUtilsTest.readAndParseFile ( self.m_edObtainedOutputDataFile )
EDVerbose.DEBUG("Checking obtained result...")
xsDataResultReference = XSDataResultDiffractionCT.parseString(strExpectedOutput)
xsDataResultObtained = plugin.getDataOutput()# XSDataResultDiffractionCT.parseString(strObtainedOutput)
EDAssert.equal(xsDataResultReference.marshal(), xsDataResultObtained.marshal())
ref = self.readAndParseFile(os.path.join(self.getTestsDataImagesHome(), "DCT2011March.chi"))
obt = self.readAndParseFile(xsDataResultObtained.getIntegratedIntensities().getPath().getValue())
EDAssert.strAlmostEqual(ref, obt, "Chi files are the same", 0.001)
# clean up SPD when finished
EDFactoryPluginStatic.loadPlugin("EDPluginSPDCorrectv10").killAllWorkers()
def runMXv1Pipeline():
strLogFileName = os.path.join(returnWorkingDirectory(), "wsgi-server.log")
EDVerbose.setLogFileName(strLogFileName)
strInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if strInput:
# Take the parameters string, split off the title and run the bash script to generate the input char. XML
listParams = shlex.split(strInput)
strComments = listParams[0] # the 1st item
strShortComments = listParams[1] # the 2nd item
strWorkingDir = listParams[2] # the 3rd item
strHTMLResultDir = listParams[3] # the 4th item
os.chdir(strWorkingDir)
strParamString = " ".join(listParams[4:]) # all but the first four items
edPluginMxv1ParamsToXML = EDFactoryPluginStatic.loadPlugin('EDPluginMxv1ParamsToXMLv1_0')
edPluginMxv1ParamsToXML.setDataInput(XSDataString(strParamString), "paramString")
edPluginMxv1ParamsToXML.executeSynchronous()
xsDataFile = edPluginMxv1ParamsToXML.getDataOutput()
# Read the XML and parse it into an object hierarchy
strXMLFile = xsDataFile.getPath().getValue()
f = open(strXMLFile, 'r')
xml = f.read()
f.close()
xsDataInputCharacterisation = XSDataInputCharacterisation.parseString(xml)
# Run the MXv1 application pipeline
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath, \
_xsDataInputCharacterisation=xsDataInputCharacterisation, \
_strComments=strComments, \
_strShortComments=strShortComments)
edApplicationMXv1Characterisation.execute()
# Run the EDNA2HTML generator on the output from the MXv1 application
edPluginExecOutputHTML = EDFactoryPluginStatic.loadPlugin('EDPluginExecOutputHTMLv1_0')
edPluginExecOutputHTML.setDataInput(XSDataString(strComments), "title")
strWorkingDir = os.path.join(strWorkingDir, edApplicationMXv1Characterisation.getWorkingDir())
edPluginExecOutputHTML.setDataInput(XSDataString(strWorkingDir), "workingDir")
#strBaseDir = os.path.join(strHTMLResultDir, "edna")
#edPluginExecOutputHTML.setDataInput(XSDataString(strBaseDir), "basename")
edPluginExecOutputHTML.setDataInput(XSDataString(strHTMLResultDir), "basename")
edPluginExecOutputHTML.executeSynchronous()
strPathToHTMLFile = ""
if (edPluginExecOutputHTML.hasDataOutput("htmlFile")):
strPathToHTMLFile = edPluginExecOutputHTML.getDataOutput("htmlFile")[0].getPath().getValue()
else:
EDVerbose.ERROR("edna-mxv1-wsgi-server: edPluginExecOutputHTML has no dataOutput htmlFile!")
if strPathToHTMLFile =="":
EDVerbose.ERROR("edna-mxv1-wsgi-server: Returning empty string")
return strPathToHTMLFile
else:
return strInput
def process(self):
"""
Calls the Plugin to be executed
"""
EDVerbose.DEBUG("EDApplicationXAFSDataProcessing.process")
if (not self.isFailure()) and (self.__bProcess):
edPlugin = EDFactoryPluginStatic.loadPlugin(self.getPluginName())
if (edPlugin is not None):
edPlugin.setBaseDirectory(
self.getFullApplicationWorkingDirectory())
edPlugin.setBaseName(self.getPluginName())
self.setPluginInput(edPlugin)
edPlugin.connectSUCCESS(self.doSuccessActionPlugin)
edPlugin.connectFAILURE(self.doFailureActionPlugin)
EDVerbose.DEBUG(
"EDApplicationXAFSDataProcessing.process: Executing " +
self.getPluginName())
edPlugin.execute()
edPlugin.synchronize()
else:
EDVerbose.error(
"EDApplicationXAFSDataProcessing .process : plugin not loaded : %s"
% self.getPluginName())
self.setFailure(True)
def preProcess(self):
"""
Initialize the plugin to be launched
"""
EDTestCasePlugin.preProcess(self)
if(EDUtilsPath.EDNA_SITE == None):
raise RuntimeError, "EDNA_SITE must be set"
# Load the plugin that should be executed
self._edPlugin = EDFactoryPluginStatic.loadPlugin(self.getPluginName())
if(self._edPlugin is not None):
for strInputDataKey in self._dictStrDataInputFiles.keys():
if (type(self._dictStrDataInputFiles[ strInputDataKey ]) == types.ListType):
for strDataInputFile in self._dictStrDataInputFiles[ strInputDataKey ]:
strXMLData = self.readAndParseFile(strDataInputFile)
if (strInputDataKey == self._strDefaultInputDataKey):
self._edPlugin.setDataInput(strXMLData)
else:
self._edPlugin.setDataInput(strXMLData, strInputDataKey)
else:
strXMLData = self.readAndParseFile(self._dictStrDataInputFiles[ strInputDataKey ])
if (strInputDataKey == self._strDefaultInputDataKey):
self._edPlugin.setDataInput(strXMLData)
else:
self._edPlugin.setDataInput(strXMLData, strInputDataKey)
#self._edPlugin.setDataInput( self._strXMLData, "inputMXCuBE" )
else:
EDVerbose.ERROR("Cannot load plugin: %s" % self.getPluginName())
raise RuntimeError
self._edPlugin.setConfiguration(self.getPluginConfiguration())
def process(self):
"""
Calls the Plugin to be executed
"""
EDVerbose.DEBUG("EDApplicationDimplev0.process")
if (not self.isFailure()):
edPlugin = EDFactoryPluginStatic.loadPlugin(self.getPluginName())
if (edPlugin is not None):
edPlugin.setBaseDirectory(
self.getFullApplicationWorkingDirectory())
edPlugin.setBaseName(self.getPluginName())
if self.ccp4DataInputControlPipelineCalcDiffMap is None:
self.ccp4DataInputControlPipelineCalcDiffMap = self.createInput(
)
edPlugin.setDataInput(
self.ccp4DataInputControlPipelineCalcDiffMap)
edPlugin.connectSUCCESS(self.doSuccessActionPlugin)
edPlugin.connectFAILURE(self.doFailureActionPlugin)
EDVerbose.DEBUG("EDApplicationDimplev0.process: Executing " +
self.getPluginName())
edPlugin.execute()
edPlugin.synchronize()
else:
EDVerbose.error(
"EDApplicationDimplev0.process : plugin not loaded : %s" %
self.getPluginName())
self.setFailure(True)
def preProcess(self):
"""
PreProcess of the execution test: download an EDF file from http://www.edna-site.org
"""
EDTestCasePluginExecuteControlMedianFilterImagev1_0.preProcess(self)
self.loadTestImage([ "noise2.edf", "noise3.edf", "noise4.edf", "noise5.edf", "noise6.edf"])
acc = EDFactoryPluginStatic.loadPlugin("EDPluginAccumulatorv1_0")
xsdIn = XSDataInputAccumulator()
xsdIn.setItem([XSDataString(os.path.join(self.getTestsDataImagesHome(), "noise%i.edf" % i)) for i in [2, 3, 5, 6]])
acc.setDataInput(xsdIn)
acc.executeSynchronous()
def runXAFSPipeline():
xmlXSDataInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if xmlXSDataInput:
edPluginControlXAFSDataProcessing = EDFactoryPluginStatic.loadPlugin('EDPluginControlXAFSDataBatchProcessingv0_1')
edPluginControlXAFSDataProcessing.setDataInput(xmlXSDataInput)
edPluginControlXAFSDataProcessing.executeSynchronous()
return os.path.join(edPluginControlXAFSDataProcessing.getWorkingDirectory(), \
edPluginControlXAFSDataProcessing.returnResultsFilename())
else:
return xmlXSDataInput
def runXAFSPipeline():
xmlXSDataInput = str(request['wsgi.input'].read(
int(request['CONTENT_LENGTH'])))
if xmlXSDataInput:
edPluginControlXAFSDataProcessing = EDFactoryPluginStatic.loadPlugin(
'EDPluginControlXAFSDataBatchProcessingv0_1')
edPluginControlXAFSDataProcessing.setDataInput(xmlXSDataInput)
edPluginControlXAFSDataProcessing.executeSynchronous()
return os.path.join(edPluginControlXAFSDataProcessing.getWorkingDirectory(), \
edPluginControlXAFSDataProcessing.returnResultsFilename())
else:
return xmlXSDataInput
def cleanUp(self, listMethods=[]):
"""
Final hook if you need to execute something after all processes finished (like killAllWorkers in SPD)
@param listMethods: allows to finish some things in the plugin.
@type listMethods: list of strings representing names of methods of the plugin to be called.
"""
self.waitForAllProcessToFinish()
edPlugin = EDFactoryPluginStatic.loadPlugin(self.__strPluginName)
for strOneMethod in listMethods:
try:
print "calling edPlugin.%s" % strOneMethod
exec "edPlugin.%s" % strOneMethod
except:
print "error in processing %s" % strOneMethod
def process(self):
"""
Calls the Plugin to be executed
"""
if (not self.__bIsFailure):
self.__edPlugin = EDFactoryPluginStatic.loadPlugin(self.__strPluginName)
if(self.__edPlugin is not None):
self.__edPlugin.setBaseDirectory(self.__strFullApplicationWorkingDirectory)
self.__edPlugin.setBaseName(self.__strPluginName)
self.__edPlugin.setDataInput(self.__strXMLData)
self.__edPlugin.connectSUCCESS(self.doSuccessActionPlugin)
self.__edPlugin.connectFAILURE(self.doFailureActionPlugin)
EDVerbose.DEBUG("EDApplication.process: Executing " + self.__strPluginName)
self.__edPlugin.execute()
self.__edPlugin.synchronize()
else:
EDVerbose.error(EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % ('EDApplication.process', self.__strPluginName))
self.__bIsFailure = True
def preProcess(self):
"""
PreProcess of the execution test: download an EDF file from http://www.edna-site.org
"""
EDTestCasePluginExecuteControlMedianFilterImagev1_0.preProcess(self)
self.loadTestImage([
"noise2.edf", "noise3.edf", "noise4.edf", "noise5.edf",
"noise6.edf"
])
acc = EDFactoryPluginStatic.loadPlugin("EDPluginAccumulatorv1_0")
xsdIn = XSDataInputAccumulator()
xsdIn.setItem([
XSDataString(
os.path.join(self.getTestsDataImagesHome(), "noise%i.edf" % i))
for i in [2, 3, 5, 6]
])
acc.setDataInput(xsdIn)
acc.executeSynchronous()
def loadPlugin(self, _strPluginToBeControlledName=None, _strBaseName=None):
"""
This method loads and returns a reference to the plugin to be controlled.
The name of the plugin to be controlled can either be passed as an
argument, or bet set before calling this method using the
"setPluginToBeControlledName".
The base name of the plugin to be controlled is used as the working
directory name of the plugin in question. If no argument is supplied
the name of the plugin is used as base name. In the case of creation of
several plugins to be launched simultaneously, the base name should be
different for each plugin and hence must be provided explicitly.
"""
EDVerbose.DEBUG("EDPluginControl.loadPlugin")
if (_strPluginToBeControlledName is None):
strPluginName = self.__strPluginToBeControlledName
else:
strPluginName = _strPluginToBeControlledName
edPlugin = EDFactoryPluginStatic.loadPlugin(strPluginName)
if (edPlugin is None):
strErrorMessage = "EDPluginControl.loadPlugin : Cannot load plugin %s" % strPluginName
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.__listOfLoadedPlugins.append(edPlugin)
edPlugin.setBaseDirectory(self.getWorkingDirectory())
if (_strBaseName is None):
# Check if base name exists. OBS! Not thread safe so please set explicitly
# _strBaseName for multi-threaded code
strRenamedPlugin = self.compactPluginName(strPluginName)
strNewWorkingDirectory = os.path.join(self.getWorkingDirectory(),
strRenamedPlugin)
if (os.path.exists(strNewWorkingDirectory)):
edPlugin.setBaseName(edPlugin.createBaseName())
else:
edPlugin.setBaseName(strRenamedPlugin)
else:
edPlugin.setBaseName(_strBaseName)
return edPlugin
def process(self):
"""
Calls the Plugin to be executed
"""
EDVerbose.DEBUG("EDApplicationXAFSBatchProcessing.process")
if (not self.isFailure()) and (self.__bProcess):
self.__edPlugin = EDFactoryPluginStatic.loadPlugin(self.getPluginName())
if(self.__edPlugin is not None):
self.__edPlugin.setBaseDirectory(self.getFullApplicationWorkingDirectory())
self.__edPlugin.setBaseName(self.getPluginName())
self.setPluginInput(self.__edPlugin)
self.__edPlugin.connectSUCCESS(self.doSuccessActionPlugin)
self.__edPlugin.connectFAILURE(self.doFailureActionPlugin)
EDVerbose.DEBUG("EDApplicationXAFSBatchProcessing.process: Executing " + self.getPluginName())
self.__edPlugin.execute()
self.__edPlugin.synchronize()
else:
EDVerbose.error("EDApplicationXAFSBatchProcessing .process : plugin not loaded : %s" % self.getPluginName())
self.setFailure(True)
def loadPlugins(self):
"""
This method loads and returns a list of references to the plugins to be controlled.
The name of the plugin to be controlled is set set before calling this method using the
"setControlledPluginName" method.
The base name of the plugin to be controlled is used as the working
directory name of the plugin in question. The name of the plugin is used as
base name.
"""
EDVerbose.DEBUG("EDPluginControl.loadPlugins")
listKeys = self.__dictControlledPlugins.keys()
listLoadedPlugins = []
for strKey in listKeys:
strPluginName = self.__dictControlledPlugins[strKey]
edPlugin = EDFactoryPluginStatic.loadPlugin(strPluginName)
edPlugin.setBaseDirectory(self.getWorkingDirectory())
edPlugin.setBaseName(strPluginName)
listLoadedPlugins.append(edPlugin)
return listLoadedPlugins
def loadPlugins(self):
"""
This method loads and returns a list of references to the plugins to be controlled.
The name of the plugin to be controlled is set set before calling this method using the
"setControlledPluginName" method.
The base name of the plugin to be controlled is used as the working
directory name of the plugin in question. The name of the plugin is used as
base name.
"""
EDVerbose.DEBUG("EDPluginControl.loadPlugins")
listKeys = self.__dictControlledPlugins.keys()
listLoadedPlugins = []
for strKey in listKeys:
strPluginName = self.__dictControlledPlugins[strKey]
edPlugin = EDFactoryPluginStatic.loadPlugin(strPluginName)
edPlugin.setBaseDirectory(self.getWorkingDirectory())
edPlugin.setBaseName(strPluginName)
listLoadedPlugins.append(edPlugin)
return listLoadedPlugins
def loadPlugin(self, _strPluginToBeControlledName=None, _strBaseName=None):
"""
This method loads and returns a reference to the plugin to be controlled.
The name of the plugin to be controlled can either be passed as an
argument, or bet set before calling this method using the
"setPluginToBeControlledName".
The base name of the plugin to be controlled is used as the working
directory name of the plugin in question. If no argument is supplied
the name of the plugin is used as base name. In the case of creation of
several plugins to be launched simultaneously, the base name should be
different for each plugin and hence must be provided explicitly.
"""
EDVerbose.DEBUG("EDPluginControl.loadPlugin")
if (_strPluginToBeControlledName is None):
strPluginName = self.__strPluginToBeControlledName
else:
strPluginName = _strPluginToBeControlledName
edPlugin = EDFactoryPluginStatic.loadPlugin(strPluginName)
if (edPlugin is None):
strErrorMessage = "EDPluginControl.loadPlugin : Cannot load plugin %s" % strPluginName
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.__listOfLoadedPlugins.append(edPlugin)
edPlugin.setBaseDirectory(self.getWorkingDirectory())
if (_strBaseName is None):
# Check if base name exists. OBS! Not thread safe so please set explicitly
# _strBaseName for multi-threaded code
strRenamedPlugin = self.compactPluginName(strPluginName)
strNewWorkingDirectory = os.path.join(self.getWorkingDirectory(), strRenamedPlugin)
if (os.path.exists(strNewWorkingDirectory)):
edPlugin.setBaseName(edPlugin.createBaseName())
else:
edPlugin.setBaseName(strRenamedPlugin)
else:
edPlugin.setBaseName(_strBaseName)
return edPlugin
def process(self):
"""
Calls the Plugin to be executed
"""
EDVerbose.DEBUG("EDApplicationDimplev0.process")
if (not self.isFailure()):
edPlugin = EDFactoryPluginStatic.loadPlugin(self.getPluginName())
if(edPlugin is not None):
edPlugin.setBaseDirectory(self.getFullApplicationWorkingDirectory())
edPlugin.setBaseName(self.getPluginName())
if self.ccp4DataInputControlPipelineCalcDiffMap is None:
self.ccp4DataInputControlPipelineCalcDiffMap = self.createInput()
edPlugin.setDataInput(self.ccp4DataInputControlPipelineCalcDiffMap)
edPlugin.connectSUCCESS(self.doSuccessActionPlugin)
edPlugin.connectFAILURE(self.doFailureActionPlugin)
EDVerbose.DEBUG("EDApplicationDimplev0.process: Executing " + self.getPluginName())
edPlugin.execute()
edPlugin.synchronize()
else:
EDVerbose.error("EDApplicationDimplev0.process : plugin not loaded : %s" % self.getPluginName())
self.setFailure(True)
serialNumber = int(dictMatch["serialNumber"])
imageNumber = int(dictMatch["imageNumber"])
listSerialNumber.append((serialNumber, imageNumber))
if firstSerialNumber is None or firstSerialNumber > serialNumber:
firstSerialNumber = serialNumber
for serialNumber, imageNumber in listSerialNumber:
imagePath = "{0}_{1:04d}.h5".format(imagePrefixAndRunNumber,
int(imageNumber))
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(
XSDataString(os.path.join(imageDirectory, imagePath)))
newImageNumber = serialNumber - firstSerialNumber + 1
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(1)
xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(serialNumber)
xsDataInputControlH5ToCBF.forcedOutputImageNumber = XSDataInteger(
newImageNumber)
edPlugin = EDFactoryPluginStatic.loadPlugin("EDPluginControlH5ToCBFv1_1")
edPlugin.dataInput = xsDataInputControlH5ToCBF
edPlugin.setBaseDirectory(pluginBaseDir)
edPlugin.setBaseName(baseName)
edPlugin.executeSynchronous()
#
# Now the edApplicationMXv1Characterisation can be imported and started
#
from EDApplicationMXv1Characterisation import EDApplicationMXv1Characterisation
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath)
edApplicationMXv1Characterisation.execute()
import sys
sys.path.append("/opt/pxsoft/EDNA/vMX/edna/kernel/src")
from EDFactoryPluginStatic import EDFactoryPluginStatic
from XSDataCommon import XSDataString
from XSDataCommon import XSDataFile
EDFactoryPluginStatic.loadModule("XSDataCCP4v1_0")
from XSDataCCP4v1_0 import XSDataInputDimple
xsDataInputDimple = XSDataInputDimple()
xsDataInputDimple.mtz = XSDataFile(
XSDataString(
"/mntdirect/_sware/exp/pxsoft/EDNA/vMX/edna/tests/data/images/dimple_noanom_aimless.mtz"
))
xsDataInputDimple.pdb = XSDataFile(
XSDataString(
"/mntdirect/_sware/exp/pxsoft/EDNA/vMX/edna/tests/data/images/dimple_model.pdb"
))
edPluginExecDimple = EDFactoryPluginStatic.loadPlugin("EDPluginExecDimplev1_0")
edPluginExecDimple.dataInput = xsDataInputDimple
edPluginExecDimple.executeSynchronous()
print(edPluginExecDimple.dataOutput.marshal())
print edPluginExecDimple.dataOutput.refmac5restrLog
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
strArgPath = strArg
if os.path.dirname(strArgPath) == "":
strArgPath = os.path.join(strCwd, strArg)
strArgPathAbsolute = os.path.abspath(strArgPath)
if os.path.exists(strArgPathAbsolute):
listPaths.append(strArgPathAbsolute)
if listPaths == []:
EDVerbose.ERROR("No valid XML file given as input!")
EDVerbose.ERROR("Arguments: %r" % sys.argv)
EDVerbose.ERROR("Usage: edna-autoproc2ispyb path_to_xml_file [--debug]")
sys.exit(1)
for strPath in listPaths:
EDVerbose.screen("Starting EDNA AutoProc -> ISPyB for file %s" % strPath)
xsDataInputStoreAutoProc = XSDataInputStoreAutoProc()
strXMLAutoProcContainer = EDUtilsFile.readFile(strPath)
xsDataAutoProcContainer = AutoProcContainer.parseString(strXMLAutoProcContainer)
if xsDataAutoProcContainer is None:
EDVerbose.WARNING("Couldn't parse file %s" % strPath)
else:
xsDataInputStoreAutoProc.setAutoProcContainer(xsDataAutoProcContainer)
edPluginISPyBStoreAutoProc = EDFactoryPluginStatic.loadPlugin("EDPluginISPyBStoreAutoProcv1_4")
edPluginISPyBStoreAutoProc.setDataInput(xsDataInputStoreAutoProc)
edPluginISPyBStoreAutoProc.connectSUCCESS(successAction)
edPluginISPyBStoreAutoProc.connectFAILURE(failureAction)
edPluginISPyBStoreAutoProc.executeSynchronous()
def preProcess(self, ):
self.edluginHDF5 = EDFactoryPluginStatic.loadPlugin("EDPluginHDF5")
pyStrEdnaHomePath = os.sep.join(pyLPath[:-5])
else:
print ("Problem in the EDNA_HOME path ..." + pyStrEdnaHomePath)
sys.exit()
os.environ["EDNA_HOME"] = pyStrEdnaHomePath
sys.path.append(os.path.join(os.environ["EDNA_HOME"], "kernel", "src"))
sys.path.append(os.path.join(os.environ["EDNA_HOME"], "kernel", "tests", "src"))
from EDVerbose import EDVerbose
from EDParallelExecute import EDParallelExecute
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("XSDataID11v1_0")
edPluginSPD = EDFactoryPluginStatic.loadPlugin("EDPluginSPDCakev1_5")
from XSDataID11v1_0 import XSDataInputID11, XSDataFile, XSDataString, XSDataBoolean
EDNAPluginName = "EDPluginControlID11v1_0"
xsdParam = XSDataFile()
xsdOutputDir = None
xsdCorrectMask = None
def fileName2xml(filename):
"""Here we create the XML string to be passed to the EDNA plugin from the input filename
This can / should be modified by the final user
@param filename: full path of the input file
@type filename: python string representing the path
@rtype: XML string
@return: python string
def run(token, projectId, runId, pdbFileId, mtzFileId, **kwargs):
startDate = datetime.datetime.now()
dstPdbFileName = 'pdbFile.pdb'
dstMtzFileName = 'mtz.mtz'
# Config file
config = ConfigParser.ConfigParser()
config.read(
'/users/opd29/passerelle-edm/scripts/extispyb/extispyb.properties')
# Connection parameters
urlExtISPyB = config.get('Connection', 'urlExtISPyB')
urlISPyB = config.get('Connection', 'urlISPyB')
# Creating Working folder
workingFolder = prepareWorkingFolder()
# Getting PDB input
os.chdir(workingFolder)
filePdbUrl = "%s/rest/file/%s/download" % (urlExtISPyB, pdbFileId)
urllib.urlretrieve(filePdbUrl, dstPdbFileName)
# Getting MTZ input
fileMtzUrl = "%s/rest/file/%s/download" % (urlExtISPyB, mtzFileId)
urllib.urlretrieve(fileMtzUrl, dstMtzFileName)
xsDataInputDimple = XSDataInputDimple()
xsDataInputDimple.mtz = XSDataFile(
XSDataString(workingFolder + "/" + dstMtzFileName))
xsDataInputDimple.pdb = XSDataFile(
XSDataString(workingFolder + "/" + dstPdbFileName))
edPluginExecDimple = EDFactoryPluginStatic.loadPlugin(
"EDPluginExecDimplev1_0")
edPluginExecDimple.dataInput = xsDataInputDimple
edPluginExecDimple.executeSynchronous()
# Uploading files
ids = []
for i in range(len(edPluginExecDimple.dataOutput.getBlob())):
ids.append(
uploadFile(
urlExtISPyB,
edPluginExecDimple.dataOutput.getBlob()
[i].getPath().getValue(), "blob"))
ids.append(
uploadFile(
urlExtISPyB,
edPluginExecDimple.dataOutput.getFinalMtz().getPath().getValue(),
"finalMtz"))
ids.append(
uploadFile(
urlExtISPyB,
edPluginExecDimple.dataOutput.getFinalPdb().getPath().getValue(),
"finalPdb"))
ids.append(
uploadFile(urlExtISPyB,
edPluginExecDimple.dataOutput.getLog().getPath().getValue(),
"log"))
ids.append(
uploadFile(
urlExtISPyB,
edPluginExecDimple.dataOutput.getFindBlobsLog().getPath().getValue(
), "findBlobsLog"))
ids.append(
uploadFile(
urlExtISPyB,
edPluginExecDimple.dataOutput.getRefmac5restrLog().getPath().
getValue(), "refmac5restrLog"))
#ids = uploadFiles(urlExtISPyB, files)
# Upload results
url = urlExtISPyB + "/rest/{token}/project/" + projectId + "/run/" + runId + "/job/add"
params = {
'name': 'Dimple',
'startDate': startDate,
'endDate': datetime.datetime.now(),
'version': 'v2.8.3 (r2962)',
'output': json.dumps(ids),
'status': 'FINISHED'
}
r = requests.post(url, data=params)
if r.status_code == 200:
setFinished(projectId, urlExtISPyB, runId)
else:
setError(projectId, urlExtISPyB, runId)
return {
"ids": ids,
"Output": edPluginExecDimple.dataOutput.marshal(),
"dstMtzFileName": dstMtzFileName,
"dstPdbFileName": dstPdbFileName
}
def initPlugin(self, strPluginName):
plugin = EDFactoryPluginStatic.loadPlugin(strPluginName)
if plugin is None:
return "Plugin not found: %s" % strPluginName
else:
return "Plugin loaded: %s" % strPluginName
dictMatch = m.groupdict()
serialNumber = int(dictMatch["serialNumber"])
imageNumber = int(dictMatch["imageNumber"])
listSerialNumber.append((serialNumber, imageNumber))
if firstSerialNumber is None or firstSerialNumber > serialNumber:
firstSerialNumber = serialNumber
for serialNumber, imageNumber in listSerialNumber:
imagePath = "{0}_{1:04d}.h5".format(imagePrefixAndRunNumber, int(imageNumber))
xsDataInputControlH5ToCBF = XSDataInputControlH5ToCBF()
xsDataInputControlH5ToCBF.hdf5File = XSDataFile(XSDataString(os.path.join(imageDirectory, imagePath)))
newImageNumber = serialNumber - firstSerialNumber + 1
xsDataInputControlH5ToCBF.imageNumber = XSDataInteger(1)
xsDataInputControlH5ToCBF.hdf5ImageNumber = XSDataInteger(serialNumber)
xsDataInputControlH5ToCBF.forcedOutputImageNumber = XSDataInteger(newImageNumber)
edPlugin = EDFactoryPluginStatic.loadPlugin("EDPluginControlH5ToCBFv1_1")
edPlugin.dataInput = xsDataInputControlH5ToCBF
edPlugin.setBaseDirectory(pluginBaseDir)
edPlugin.setBaseName(baseName)
edPlugin.executeSynchronous()
#
# Now the edApplicationMXv1Characterisation can be imported and started
#
from EDApplicationMXv1Characterisation import EDApplicationMXv1Characterisation
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath)
edApplicationMXv1Characterisation.execute()
sys.exit(1)
for strPath in listPaths:
EDVerbose.screen("Starting EDNA AutoProc -> ISPyB for file %s" %
strPath)
xsDataInputStoreAutoProc = XSDataInputStoreAutoProc()
strXMLAutoProcContainer = EDUtilsFile.readFile(strPath)
xsDataAutoProcContainer = AutoProcContainer.parseString(
strXMLAutoProcContainer)
if xsDataAutoProcContainer is None:
EDVerbose.WARNING("Couldn't parse file %s" % strPath)
else:
if xsDataAutoProcContainer.AutoProcProgramContainer.AutoProcProgram.processingStatus == "True":
xsDataAutoProcContainer.AutoProcProgramContainer.AutoProcProgram.processingStatus = "SUCCESS"
xsDataInputStoreAutoProc.setAutoProcContainer(
xsDataAutoProcContainer)
edPluginISPyBStoreAutoProc = EDFactoryPluginStatic.loadPlugin(
"EDPluginISPyBStoreAutoProcv1_4")
edPluginISPyBStoreAutoProc.setDataInput(xsDataInputStoreAutoProc)
edPluginISPyBStoreAutoProc.executeSynchronous()
if edPluginISPyBStoreAutoProc.isFailure():
EDVerbose.ERROR("XML data not stored in ISPyB")
else:
xsDataResultISPyBStoreAutoProc = edPluginISPyBStoreAutoProc.dataOutput
EDVerbose.screen("XML data sucessfully stored in ISPyB")
if xsDataResultISPyBStoreAutoProc.autoProcScalingId is not None:
EDVerbose.screen(
"autoProcScalingId: %d" %
xsDataResultISPyBStoreAutoProc.autoProcScalingId.value)
else:
EDVerbose.warning("No autoProcScalingId in results!")
from XSDataGridScreeningv1_0 import XSDataInputGridScreening
if __name__ == '__main__':
strPathToTempDir = tempfile.mkdtemp(prefix="edna-image-quality-indicators_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "edna.log"))
# Popolate input data
EDVerbose.screen("Starting EDNA image quality indicators processing")
EDVerbose.screen("Arguments: %r" % sys.argv)
bVerbose = False
bDebug = False
listPaths = []
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
if os.path.exists(strArg):
listPaths.append(os.path.abspath(strArg))
for strPath in listPaths:
xsDataInputGridScreening = XSDataInputGridScreening()
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(strPath))
xsDataInputGridScreening.setImageFile(xsDataFile)
xsDataInputGridScreening.setDoOnlyImageQualityIndicators(XSDataBoolean(True))
xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(XSDataBoolean(True))
edPluginGridScreening = EDFactoryPluginStatic.loadPlugin("EDPluginControlGridScreeningv1_0")
edPluginGridScreening.setDataInput(xsDataInputGridScreening)
edPluginGridScreening.executeSynchronous()
def loadPlugin(cls, _strPluginName):
EDVerbose.WARNING("The use of EDApplication.loadPlugin is deprecated. Please use EDFactoryPluginStatic.getFactoryPlugin instead.")
return EDFactoryPluginStatic.loadPlugin(_strPluginName)
strPathToTempDir = tempfile.mkdtemp(
prefix="edna-image-quality-indicators_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "edna.log"))
# Popolate input data
EDVerbose.screen("Starting EDNA image quality indicators processing")
EDVerbose.screen("Arguments: %r" % sys.argv)
bVerbose = False
bDebug = False
listPaths = []
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
if os.path.exists(strArg):
listPaths.append(os.path.abspath(strArg))
for strPath in listPaths:
xsDataInputGridScreening = XSDataInputGridScreening()
xsDataFile = XSDataFile()
xsDataFile.setPath(XSDataString(strPath))
xsDataInputGridScreening.setImageFile(xsDataFile)
xsDataInputGridScreening.setDoOnlyImageQualityIndicators(
XSDataBoolean(True))
xsDataInputGridScreening.setStoreImageQualityIndicatorsInISPyB(
XSDataBoolean(True))
edPluginGridScreening = EDFactoryPluginStatic.loadPlugin(
"EDPluginControlGridScreeningv1_0")
edPluginGridScreening.setDataInput(xsDataInputGridScreening)
edPluginGridScreening.executeSynchronous()
def preProcess(self,):
self.edluginHDF5 = EDFactoryPluginStatic.loadPlugin("EDPluginHDF5")
def runMXv1Pipeline():
strLogFileName = os.path.join(returnWorkingDirectory(), "wsgi-server.log")
EDVerbose.setLogFileName(strLogFileName)
strInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if strInput:
# Take the parameters string, split off the title and run the bash script to generate the input char. XML
listParams = shlex.split(strInput)
strComments = listParams[0] # the 1st item
strShortComments = listParams[1] # the 2nd item
strWorkingDir = listParams[2] # the 3rd item
strHTMLResultDir = listParams[3] # the 4th item
os.chdir(strWorkingDir)
strParamString = " ".join(
listParams[4:]) # all but the first four items
edPluginMxv1ParamsToXML = EDFactoryPluginStatic.loadPlugin(
'EDPluginMxv1ParamsToXMLv1_0')
edPluginMxv1ParamsToXML.setDataInput(XSDataString(strParamString),
"paramString")
edPluginMxv1ParamsToXML.executeSynchronous()
xsDataFile = edPluginMxv1ParamsToXML.getDataOutput()
# Read the XML and parse it into an object hierarchy
strXMLFile = xsDataFile.getPath().getValue()
f = open(strXMLFile, 'r')
xml = f.read()
f.close()
xsDataInputCharacterisation = XSDataInputCharacterisation.parseString(
xml)
# Run the MXv1 application pipeline
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath, \
_xsDataInputCharacterisation=xsDataInputCharacterisation, \
_strComments=strComments, \
_strShortComments=strShortComments)
edApplicationMXv1Characterisation.execute()
# Run the EDNA2HTML generator on the output from the MXv1 application
edPluginExecOutputHTML = EDFactoryPluginStatic.loadPlugin(
'EDPluginExecOutputHTMLv1_0')
edPluginExecOutputHTML.setDataInput(XSDataString(strComments), "title")
strWorkingDir = os.path.join(
strWorkingDir, edApplicationMXv1Characterisation.getWorkingDir())
edPluginExecOutputHTML.setDataInput(XSDataString(strWorkingDir),
"workingDir")
#strBaseDir = os.path.join(strHTMLResultDir, "edna")
#edPluginExecOutputHTML.setDataInput(XSDataString(strBaseDir), "basename")
edPluginExecOutputHTML.setDataInput(XSDataString(strHTMLResultDir),
"basename")
edPluginExecOutputHTML.executeSynchronous()
strPathToHTMLFile = ""
if (edPluginExecOutputHTML.hasDataOutput("htmlFile")):
strPathToHTMLFile = edPluginExecOutputHTML.getDataOutput(
"htmlFile")[0].getPath().getValue()
else:
EDVerbose.ERROR(
"edna-mxv1-wsgi-server: edPluginExecOutputHTML has no dataOutput htmlFile!"
)
if strPathToHTMLFile == "":
EDVerbose.ERROR("edna-mxv1-wsgi-server: Returning empty string")
return strPathToHTMLFile
else:
return strInput
def initPlugin(self, strPluginName):
plugin = EDFactoryPluginStatic.loadPlugin(strPluginName)
if plugin is None:
return "Plugin not found: %s" % strPluginName
else:
return "Plugin loaded: %s" % strPluginName
