def createDataInputCharacterisationFromDataFiles(self, _pyListXSDataFile):
"""
This method takes as input a list of paths to XML data files. It parses
these files and create a single XSDataInputCharacterisation object.
"""
EDVerbose.DEBUG(
"EDPluginControlCCP4iv1_1.createDataInputCharacterisationFromDataFiles"
)
xsDataInputCharacterisation = None
for xsDataInputFile in _pyListXSDataFile:
try:
pyStrInputFileContent = EDUtilsFile.readFile(
xsDataInputFile.getPath().getValue())
xsDataInputCharacterisationCurrent = XSDataInputCharacterisation.parseString(
pyStrInputFileContent)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlCCP4iv1_1.preProcess',
'EDPluginControlCCP4iv1_1', detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
if (xsDataInputCharacterisationCurrent is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlCCP4iv1_1.preProcess',
'EDPluginControlCCP4iv1_1', "None data collection")
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Instantiate the xsDataInputCharacterisation object if it's not already done.
if (xsDataInputCharacterisation is None):
xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataInputCharacterisation.setDataCollection(
xsDataInputCharacterisationCurrent.getDataCollection())
def createDataInputCharacterisationFromDataFiles(self, _pyListXSDataFile):
"""
This method takes as input a list of paths to XML data files. It parses
these files and create a single XSDataInputCharacterisation object.
"""
EDVerbose.DEBUG("EDPluginControlCCP4iv1_1.createDataInputCharacterisationFromDataFiles")
xsDataInputCharacterisation = None
for xsDataInputFile in _pyListXSDataFile:
try:
pyStrInputFileContent = EDUtilsFile.readFile(xsDataInputFile.getPath().getValue())
xsDataInputCharacterisationCurrent = XSDataInputCharacterisation.parseString(pyStrInputFileContent)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlCCP4iv1_1.preProcess', 'EDPluginControlCCP4iv1_1', detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
if (xsDataInputCharacterisationCurrent is None):
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlCCP4iv1_1.preProcess', 'EDPluginControlCCP4iv1_1', "None data collection")
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Instantiate the xsDataInputCharacterisation object if it's not already done.
if (xsDataInputCharacterisation is None):
xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataInputCharacterisation.setDataCollection(xsDataInputCharacterisationCurrent.getDataCollection())
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 testSetDataInput(self):
edPluginControlCharacterisationv1_1 = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
edPluginControlCharacterisationv1_1.setConfiguration(xsPluginItemGood01)
edPluginControlCharacterisationv1_1.configure()
edStringXMLInput = self.readAndParseFile(self.strReferenceInputFile)
edPluginControlCharacterisationv1_1.setDataInput(edStringXMLInput)
from XSDataMXv1 import XSDataInputCharacterisation
xsDataInputCharacterisationReference = XSDataInputCharacterisation.parseString(edStringXMLInput)
xsDataInputCharacterisationv11 = edPluginControlCharacterisationv1_1.getDataInput()
EDAssert.equal(xsDataInputCharacterisationReference.marshal(), xsDataInputCharacterisationv11.marshal())
def testSetDataInput(self):
edPluginControlCharacterisationv1_1 = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(
os.path.join(self.getPluginTestsDataHome(), "XSConfiguration.xml"))
edPluginControlCharacterisationv1_1.setConfiguration(
xsPluginItemGood01)
edPluginControlCharacterisationv1_1.configure()
edStringXMLInput = self.readAndParseFile(self.strReferenceInputFile)
edPluginControlCharacterisationv1_1.setDataInput(edStringXMLInput)
from XSDataMXv1 import XSDataInputCharacterisation
xsDataInputCharacterisationReference = XSDataInputCharacterisation.parseString(
edStringXMLInput)
xsDataInputCharacterisationv11 = edPluginControlCharacterisationv1_1.getDataInput(
)
EDAssert.equal(xsDataInputCharacterisationReference.marshal(),
xsDataInputCharacterisationv11.marshal())
def testCheckParameters(self):
strXMLInput = self.readAndParseFile(self.strPathToReferenceInput)
xsDataInput = XSDataInputCharacterisation.parseString(strXMLInput)
edPluginExecCharacterisation = self.createPlugin()
edPluginExecCharacterisation.setDataInput(xsDataInput)
edPluginExecCharacterisation.checkParameters()
def testCheckParameters(self):
strXMLInput = self.readAndParseFile(self.strPathToReferenceInput)
xsDataInput = XSDataInputCharacterisation.parseString(strXMLInput)
edPluginExecCharacterisation = self.createPlugin()
edPluginExecCharacterisation.setDataInput(xsDataInput)
edPluginExecCharacterisation.checkParameters()
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
