class EDPluginISPyBv1_2(EDPluginExec):
"""
Plugin to store results in an ISPyB database using the DNA/ISPyB dbserver
"""
def __init__(self):
"""
Sets default values for dbserver parameters
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataISPyBScreening, "screening") # [0, 1]
self.setXSDataInputClass(XSDataISPyBScreeningInput, "screeningInput") # [0, infinite]
self.setXSDataInputClass(XSDataISPyBScreeningOutputContainer, "screeningOutputContainer") # [0, infinite]
self.setXSDataInputClass(XSDataISPyBScreeningRank, "screeningRank") # [0, infinite]
self.setXSDataInputClass(XSDataISPyBScreeningRankSet, "screeningRankSet") # [0, 1]
self.setXSDataInputClass(XSDataISPyBScreeningFile, "screeningFile") # [0, infinite]
self.setXSDataInputClass(XSDataISPyBImage, "image") # [0, 1]
self.__strDbserverHost = "localhost"
self.__iDbserverPort = 9090
def getDbserverHost(self):
return self.__strDbserverHost
def setDbserverHost(self, _strDbserverHost):
self.__strDbserverHost = _strDbserverHost
def getDbserverPort(self):
return self.__iDbserverPort
def setDbserverPort(self, _iDbserverPort):
self.__iDbserverPort = _iDbserverPort
def configure(self):
"""
Gets the dbserver parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
pluginConfiguration = self.getConfiguration()
if(pluginConfiguration == None):
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.configure: pluginConfiguration is None, using default settings")
else:
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.configure: pluginConfiguration found, using settings from there")
strDbserverHost = EDConfiguration.getStringParamValue(pluginConfiguration, "dbserverHost")
if(strDbserverHost == None):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2.configure", self.getClassName(), \
"Configuration parameter missing: dbserverHost")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.setDbserverHost(strDbserverHost)
strDbserverPort = EDConfiguration.getStringParamValue(pluginConfiguration, "dbserverPort")
if(strDbserverPort == None):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2.configure", self.getClassName(), \
"Configuration parameter missing: dbserverPort")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.setDbserverPort(int (strDbserverPort))
def process(self, _edObject=None):
"""
Sends store requests with the screening objects to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput("inputISPyB")[0] will be stored.
* Primary key attributes should not be set.
* If a foreign key attribute is not set, this method will attempt to find the foreign object among the
input objects, and then use the primary key attribute of this object when it has been stored. If such
an object is not found, the method fails.
* If an error is encountered, the method will immediately fail and will not attempt to store any more
objects.
"""
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.process")
# Basic sanity check of inputs:
if (self.hasDataInput("screening")):
if (len(self.getDataInput("screening")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", "There should only be one input 'screening'.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if (self.hasDataInput("screeningRankSet")):
if (len(self.getDataInput("screeningRankSet")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", "There should only be one input 'screeningRankSet'.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Get the inputs
xsDataISPyBScreenings = None
xsDataISPyBScreeningInputs = None
xsDataISPyBScreeningOutputContainers = None
xsDataISPyBScreeningRanks = None
xsDataISPyBScreeningRankSets = None
xsDataISPyBImages = None
xsDataISPyBScreeningFiles = None
if self.hasDataInput("screening"):
xsDataISPyBScreenings = self.getDataInput("screening")
if self.hasDataInput("screeningInput"):
xsDataISPyBScreeningInputs = self.getDataInput("screeningInput")
if self.hasDataInput("screeningOutputContainer"):
xsDataISPyBScreeningOutputContainers = self.getDataInput("screeningOutputContainer")
if self.hasDataInput("screeningRank"):
xsDataISPyBScreeningRanks = self.getDataInput("screeningRank")
if self.hasDataInput("screeningRankSet"):
xsDataISPyBScreeningRankSets = self.getDataInput("screeningRankSet")
if self.hasDataInput("image"):
xsDataISPyBImages = self.getDataInput("image")
if self.hasDataInput("screeningFile"):
xsDataISPyBScreeningFiles = self.getDataInput("screeningFile")
self.__xsDataResultISPyB = XSDataResultISPyB()
if (xsDataISPyBScreenings is None):
xsDataISPyBScreening = XSDataISPyBScreening()
else:
xsDataISPyBScreening = xsDataISPyBScreenings[0]
if (xsDataISPyBImages is None):
xsDataISPyBImage = None
else:
xsDataISPyBImage = xsDataISPyBImages[0]
# Another sanity check:
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None) or (xsDataISPyBImage.getFileName() == None) or (xsDataISPyBImage.getFileLocation() == None)):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", \
"Neither a dataCollectionId nor an image filename + path are provided.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
strResponse = self.httpPost(self.getDbserverHost(), self.getDbserverPort(), "/get_datacollectionid", strXML)
if strResponse != None:
# Handle response:
xsDatadbstatus = XSDatadbstatus.parseString(strResponse)
strCode = xsDatadbstatus.getCode()
strMessage = xsDatadbstatus.getMessage()
EDVerbose.DEBUG("dbserver returns code: " + strCode)
EDVerbose.DEBUG("dbserver returns message: " + strMessage)
if (strCode == "error") or (xsDatadbstatus.getDataCollectionId() == -1):
if xsDatadbstatus.getDataCollectionId() == -1:
strMessage = "An image corresponding to the given fileName and fileLocation was not found."
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", strMessage)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(XSDataInteger(xsDatadbstatus.getDataCollectionId()))
self.__xsDataResultISPyB.setDataCollectionId(XSDataInteger(xsDatadbstatus.getDataCollectionId()))
if (xsDataISPyBScreeningRankSets is None):
xsDataISPyBScreeningRankSet = None
else:
xsDataISPyBScreeningRankSet = xsDataISPyBScreeningRankSets[0]
# Store all the different screening* objects:
xsDataIntegerScreeningId = self.store(xsDataISPyBScreening)
if xsDataISPyBScreeningInputs != None:
for xsDataISPyBScreeningInput in xsDataISPyBScreeningInputs:
xsDataISPyBScreeningInput.setScreeningId(xsDataIntegerScreeningId)
self.store(xsDataISPyBScreeningInput)
if xsDataISPyBScreeningRankSet != None:
xsDataIntegerScreeningRankSetId = self.store(xsDataISPyBScreeningRankSet)
for xsDataISPyBScreeningRank in xsDataISPyBScreeningRanks:
xsDataISPyBScreeningRank.setScreeningId(xsDataIntegerScreeningId)
xsDataISPyBScreeningRank.setScreeningRankSetId(xsDataIntegerScreeningRankSetId)
self.store(xsDataISPyBScreeningRank)
if xsDataISPyBScreeningOutputContainers != None:
for xsDataISPyBScreeningOutputContainer in xsDataISPyBScreeningOutputContainers:
xsDataISPyBScreeningOutput = xsDataISPyBScreeningOutputContainer.getScreeningOutput()
xsDataISPyBScreeningOutput.setScreeningId(xsDataIntegerScreeningId)
xsDataIntegerScreeningOutputId = self.store(xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputLattices = xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice()
if xsDataISPyBScreeningOutputLattices != None:
for xsDataISPyBScreeningOutputLattice in xsDataISPyBScreeningOutputLattices:
xsDataISPyBScreeningOutputLattice.setScreeningOutputId(xsDataIntegerScreeningOutputId)
self.store(xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningStrategyContainers = xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer()
if xsDataISPyBScreeningStrategyContainers != None:
for xsDataISPyBScreeningStrategyContainer in xsDataISPyBScreeningStrategyContainers:
xsDataISPyBScreeningStrategy = xsDataISPyBScreeningStrategyContainer.getScreeningStrategy()
if xsDataISPyBScreeningStrategy != None:
xsDataISPyBScreeningStrategy.setScreeningOutputId(xsDataIntegerScreeningOutputId)
xsDataIntegerScreeningStrategyId = self.store(xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningStrategyWedgeContainers = xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer()
if xsDataISPyBScreeningStrategyWedgeContainers != None:
for xsDataISPyBScreeningStrategyWedgeContainer in xsDataISPyBScreeningStrategyWedgeContainers:
xsDataISPyBScreeningStrategyWedge = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategyWedge()
xsDataISPyBScreeningStrategyWedge.setScreeningStrategyId(xsDataIntegerScreeningStrategyId)
xsDataIntegerScreeningStrategyWedgeId = self.store(xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategySubWedges = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge()
if xsDataISPyBScreeningStrategySubWedges != None:
for xsDataISPyBScreeningStrategySubWedge in xsDataISPyBScreeningStrategySubWedges:
xsDataISPyBScreeningStrategySubWedge.setScreeningStrategyWedgeId(xsDataIntegerScreeningStrategyWedgeId)
self.store(xsDataISPyBScreeningStrategySubWedge)
def postProcess(self, _edObject=None):
"""
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.postProcess")
if (self.__xsDataResultISPyB is not None):
self.setDataOutput(self.__xsDataResultISPyB)
def httpPost(self, _strHost, _iPort, _strPath, _strXML):
"""
Sends XML to the dbserver on the specified host and port with the specified path.
Returns the response XML from the dbserver.
@param _strHost: the host name for the dbserver
@type _strHost: string
@param _iPort: the port for the dbserver
@type _iPort: integer
@param _strPath: the path name for the request
@type _strPath: string
@param _strXML: the XML for the request
@type _strXML: string
"""
strData = None
try:
pyHTTPConnection = httplib.HTTPConnection(_strHost, _iPort)
pyHTTPConnection.putrequest("POST", _strPath)
pyHTTPConnection.putheader("Content-type", "text/xml")
pyHTTPConnection.putheader("Content-length", "%d" % len(_strXML))
pyHTTPConnection.putheader('Accept', 'text/plain')
if "HOSTNAME" in os.environ.keys():
pyHTTPConnection.putheader('Host', os.environ["HOSTNAME"])
pyHTTPConnection.endheaders()
pyHTTPConnection.send(_strXML)
pyHTTPResponse = pyHTTPConnection.getresponse()
strMsg = pyHTTPResponse.msg
strHeaders = pyHTTPResponse.getheaders()
strReply = str(pyHTTPResponse.status) + ' - ' + pyHTTPResponse.reason
strContentLength = pyHTTPResponse.getheader("Content-Length")
if strContentLength is None:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "httpPost", \
"No header returned for %s, host %s, port %d. HTTP resonse was: %s" \
% (_strPath, _strHost, _iPort, strReply))
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
try:
ilength = string.atoi(strContentLength)
except:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "httpPost", \
"Cannot convert Content-Length %s to integer for %s, host %s, port %d!" \
% (strContentLength, _strPath, _strHost, _iPort))
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
strData = pyHTTPResponse.read()
except (socket.error, httplib.BadStatusLine), (msg):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "httpPost", \
"Have you set up a connection to the dbserver? Error is: %s" % (msg))
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise RuntimeError, strErrorMessage
return strData
def process(self, _edObject=None):
"""
Sends store requests with the screening objects to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput("inputISPyB")[0] will be stored.
* Primary key attributes should not be set.
* If a foreign key attribute is not set, this method will attempt to find the foreign object among the
input objects, and then use the primary key attribute of this object when it has been stored. If such
an object is not found, the method fails.
* If an error is encountered, the method will immediately fail and will not attempt to store any more
objects.
"""
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginISPyBv1_2.process")
# Basic sanity check of inputs:
if (self.hasDataInput("screening")):
if (len(self.getDataInput("screening")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", "There should only be one input 'screening'.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if (self.hasDataInput("screeningRankSet")):
if (len(self.getDataInput("screeningRankSet")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", "There should only be one input 'screeningRankSet'.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Get the inputs
xsDataISPyBScreenings = None
xsDataISPyBScreeningInputs = None
xsDataISPyBScreeningOutputContainers = None
xsDataISPyBScreeningRanks = None
xsDataISPyBScreeningRankSets = None
xsDataISPyBImages = None
xsDataISPyBScreeningFiles = None
if self.hasDataInput("screening"):
xsDataISPyBScreenings = self.getDataInput("screening")
if self.hasDataInput("screeningInput"):
xsDataISPyBScreeningInputs = self.getDataInput("screeningInput")
if self.hasDataInput("screeningOutputContainer"):
xsDataISPyBScreeningOutputContainers = self.getDataInput("screeningOutputContainer")
if self.hasDataInput("screeningRank"):
xsDataISPyBScreeningRanks = self.getDataInput("screeningRank")
if self.hasDataInput("screeningRankSet"):
xsDataISPyBScreeningRankSets = self.getDataInput("screeningRankSet")
if self.hasDataInput("image"):
xsDataISPyBImages = self.getDataInput("image")
if self.hasDataInput("screeningFile"):
xsDataISPyBScreeningFiles = self.getDataInput("screeningFile")
self.__xsDataResultISPyB = XSDataResultISPyB()
if (xsDataISPyBScreenings is None):
xsDataISPyBScreening = XSDataISPyBScreening()
else:
xsDataISPyBScreening = xsDataISPyBScreenings[0]
if (xsDataISPyBImages is None):
xsDataISPyBImage = None
else:
xsDataISPyBImage = xsDataISPyBImages[0]
# Another sanity check:
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None) or (xsDataISPyBImage.getFileName() == None) or (xsDataISPyBImage.getFileLocation() == None)):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", \
"Neither a dataCollectionId nor an image filename + path are provided.")
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
strResponse = self.httpPost(self.getDbserverHost(), self.getDbserverPort(), "/get_datacollectionid", strXML)
if strResponse != None:
# Handle response:
xsDatadbstatus = XSDatadbstatus.parseString(strResponse)
strCode = xsDatadbstatus.getCode()
strMessage = xsDatadbstatus.getMessage()
EDVerbose.DEBUG("dbserver returns code: " + strCode)
EDVerbose.DEBUG("dbserver returns message: " + strMessage)
if (strCode == "error") or (xsDatadbstatus.getDataCollectionId() == -1):
if xsDatadbstatus.getDataCollectionId() == -1:
strMessage = "An image corresponding to the given fileName and fileLocation was not found."
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", strMessage)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(XSDataInteger(xsDatadbstatus.getDataCollectionId()))
self.__xsDataResultISPyB.setDataCollectionId(XSDataInteger(xsDatadbstatus.getDataCollectionId()))
if (xsDataISPyBScreeningRankSets is None):
xsDataISPyBScreeningRankSet = None
else:
xsDataISPyBScreeningRankSet = xsDataISPyBScreeningRankSets[0]
# Store all the different screening* objects:
xsDataIntegerScreeningId = self.store(xsDataISPyBScreening)
if xsDataISPyBScreeningInputs != None:
for xsDataISPyBScreeningInput in xsDataISPyBScreeningInputs:
xsDataISPyBScreeningInput.setScreeningId(xsDataIntegerScreeningId)
self.store(xsDataISPyBScreeningInput)
if xsDataISPyBScreeningRankSet != None:
xsDataIntegerScreeningRankSetId = self.store(xsDataISPyBScreeningRankSet)
for xsDataISPyBScreeningRank in xsDataISPyBScreeningRanks:
xsDataISPyBScreeningRank.setScreeningId(xsDataIntegerScreeningId)
xsDataISPyBScreeningRank.setScreeningRankSetId(xsDataIntegerScreeningRankSetId)
self.store(xsDataISPyBScreeningRank)
if xsDataISPyBScreeningOutputContainers != None:
for xsDataISPyBScreeningOutputContainer in xsDataISPyBScreeningOutputContainers:
xsDataISPyBScreeningOutput = xsDataISPyBScreeningOutputContainer.getScreeningOutput()
xsDataISPyBScreeningOutput.setScreeningId(xsDataIntegerScreeningId)
xsDataIntegerScreeningOutputId = self.store(xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputLattices = xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice()
if xsDataISPyBScreeningOutputLattices != None:
for xsDataISPyBScreeningOutputLattice in xsDataISPyBScreeningOutputLattices:
xsDataISPyBScreeningOutputLattice.setScreeningOutputId(xsDataIntegerScreeningOutputId)
self.store(xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningStrategyContainers = xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer()
if xsDataISPyBScreeningStrategyContainers != None:
for xsDataISPyBScreeningStrategyContainer in xsDataISPyBScreeningStrategyContainers:
xsDataISPyBScreeningStrategy = xsDataISPyBScreeningStrategyContainer.getScreeningStrategy()
if xsDataISPyBScreeningStrategy != None:
xsDataISPyBScreeningStrategy.setScreeningOutputId(xsDataIntegerScreeningOutputId)
xsDataIntegerScreeningStrategyId = self.store(xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningStrategyWedgeContainers = xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer()
if xsDataISPyBScreeningStrategyWedgeContainers != None:
for xsDataISPyBScreeningStrategyWedgeContainer in xsDataISPyBScreeningStrategyWedgeContainers:
xsDataISPyBScreeningStrategyWedge = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategyWedge()
xsDataISPyBScreeningStrategyWedge.setScreeningStrategyId(xsDataIntegerScreeningStrategyId)
xsDataIntegerScreeningStrategyWedgeId = self.store(xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategySubWedges = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge()
if xsDataISPyBScreeningStrategySubWedges != None:
for xsDataISPyBScreeningStrategySubWedge in xsDataISPyBScreeningStrategySubWedges:
xsDataISPyBScreeningStrategySubWedge.setScreeningStrategyWedgeId(xsDataIntegerScreeningStrategyWedgeId)
self.store(xsDataISPyBScreeningStrategySubWedge)
def testExecute(self):
"""
Runs the plugin and then compares expected output with obtained output to verify that it executed correctly.
"""
self.run()
# Checks the obtained result against the expected result
edStringExpectedOutput = self.readAndParseFile(
self.getReferenceDataOutputFile())
edStringObtainedOutput = self.readAndParseFile(
self.__strObtainedOutputDataFile)
xsDataResultISPyBExpected = XSDataResultISPyB.parseString(
edStringExpectedOutput)
xsDataResultISPyBObtained = XSDataResultISPyB.parseString(
edStringObtainedOutput)
self.DEBUG("Checking obtained result...")
xsDataIntegerExpDataCollectionId = xsDataResultISPyBExpected.getDataCollectionId(
)
xsDataResultStatusExpScreening = xsDataResultISPyBExpected.getScreeningStatus(
)
xsDataResultStatusExpScreeningInputs = xsDataResultISPyBExpected.getScreeningInputStatus(
)
xsDataResultStatusExpScreeningOutputs = xsDataResultISPyBExpected.getScreeningOutputStatus(
)
xsDataResultStatusExpScreeningOutputLattices = xsDataResultISPyBExpected.getScreeningOutputLatticeStatus(
)
xsDataResultStatusExpScreeningStrategies = xsDataResultISPyBExpected.getScreeningStrategyStatus(
)
xsDataResultStatusExpScreeningStrategyWedges = xsDataResultISPyBExpected.getScreeningStrategyWedgeStatus(
)
xsDataResultStatusExpScreeningStrategySubWedges = xsDataResultISPyBExpected.getScreeningStrategySubWedgeStatus(
)
xsDataResultStatusExpScreeningRanks = xsDataResultISPyBExpected.getScreeningRankStatus(
)
xsDataResultStatusExpScreeningRankSet = xsDataResultISPyBExpected.getScreeningRankSetStatus(
)
xsDataIntegerDataCollectionId = xsDataResultISPyBObtained.getDataCollectionId(
)
xsDataResultStatusScreening = xsDataResultISPyBObtained.getScreeningStatus(
)
xsDataResultStatusScreeningInputs = xsDataResultISPyBObtained.getScreeningInputStatus(
)
xsDataResultStatusScreeningOutputs = xsDataResultISPyBObtained.getScreeningOutputStatus(
)
xsDataResultStatusScreeningOutputLattices = xsDataResultISPyBObtained.getScreeningOutputLatticeStatus(
)
xsDataResultStatusScreeningStrategies = xsDataResultISPyBObtained.getScreeningStrategyStatus(
)
xsDataResultStatusScreeningStrategyWedges = xsDataResultISPyBObtained.getScreeningStrategyWedgeStatus(
)
xsDataResultStatusScreeningStrategySubWedges = xsDataResultISPyBObtained.getScreeningStrategySubWedgeStatus(
)
xsDataResultStatusScreeningRanks = xsDataResultISPyBObtained.getScreeningRankStatus(
)
xsDataResultStatusScreeningRankSet = xsDataResultISPyBObtained.getScreeningRankSetStatus(
)
if xsDataIntegerExpDataCollectionId != None:
self.DEBUG("Checking dataCollectionId ...")
EDAssert.equal(xsDataIntegerDataCollectionId.getValue(),
xsDataIntegerExpDataCollectionId.getValue())
if xsDataResultStatusExpScreening != None:
self.DEBUG("Checking screening ...")
EDAssert.equal(xsDataResultStatusScreening.getCode().getValue(),
"ok")
iId = xsDataResultStatusScreening.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningInputs != None:
self.DEBUG("Checking inputs...")
for xsDataResultStatusScreeningInput in xsDataResultStatusScreeningInputs:
EDAssert.equal(
xsDataResultStatusScreeningInput.getCode().getValue(),
"ok")
iId = xsDataResultStatusScreeningInput.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningOutputs != None:
self.DEBUG("Checking outputs ...")
for xsDataResultStatusScreeningOutput in xsDataResultStatusScreeningOutputs:
EDAssert.equal(
xsDataResultStatusScreeningOutput.getCode().getValue(),
"ok")
iId = xsDataResultStatusScreeningOutput.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningOutputLattices != None:
self.DEBUG("Checking output lattices...")
for xsDataResultStatusScreeningOutputLattice in xsDataResultStatusScreeningOutputLattices:
EDAssert.equal(
xsDataResultStatusScreeningOutputLattice.getCode().
getValue(), "ok")
iId = xsDataResultStatusScreeningOutputLattice.getId(
).getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningStrategies != None:
self.DEBUG("Checking strategies...")
for xsDataResultStatusScreeningStrategy in xsDataResultStatusScreeningStrategies:
EDAssert.equal(
xsDataResultStatusScreeningStrategy.getCode().getValue(),
"ok")
iId = xsDataResultStatusScreeningStrategy.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningStrategyWedges != None:
self.DEBUG("Checking strategy wedges...")
for xsDataResultStatusScreeningStrategyWedge in xsDataResultStatusScreeningStrategyWedges:
EDAssert.equal(
xsDataResultStatusScreeningStrategyWedge.getCode().
getValue(), "ok")
iId = xsDataResultStatusScreeningStrategyWedge.getId(
).getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningStrategySubWedges != None:
self.DEBUG("Checking strategy subwedges...")
for xsDataResultStatusScreeningStrategySubWedge in xsDataResultStatusScreeningStrategySubWedges:
EDAssert.equal(
xsDataResultStatusScreeningStrategySubWedge.getCode().
getValue(), "ok")
iId = xsDataResultStatusScreeningStrategySubWedge.getId(
).getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningRanks != None:
self.DEBUG("Checking ranks...")
for xsDataResultStatusScreeningRank in xsDataResultStatusScreeningRanks:
EDAssert.equal(
xsDataResultStatusScreeningRank.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningRank.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusScreeningRankSet != None:
self.DEBUG("Checking rank sets...")
EDAssert.equal(
xsDataResultStatusScreeningRankSet.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningRankSet.getId().getValue()
EDAssert.equal((iId >= 0), True)
def testExecute(self):
"""
Runs the plugin and then compares expected output with obtained output to verify that it executed correctly.
"""
self.run()
# Checks the obtained result against the expected result
edStringExpectedOutput = self.readAndParseFile(self.getReferenceDataOutputFile())
edStringObtainedOutput = self.readAndParseFile(self.__strObtainedOutputDataFile)
xsDataResultISPyBExpected = XSDataResultISPyB.parseString(edStringExpectedOutput)
xsDataResultISPyBObtained = XSDataResultISPyB.parseString(edStringObtainedOutput)
self.DEBUG("Checking obtained result...")
xsDataIntegerExpDataCollectionId = xsDataResultISPyBExpected.getDataCollectionId()
xsDataResultStatusExpScreening = xsDataResultISPyBExpected.getScreeningStatus()
xsDataResultStatusExpScreeningInputs = xsDataResultISPyBExpected.getScreeningInputStatus()
xsDataResultStatusExpScreeningOutputs = xsDataResultISPyBExpected.getScreeningOutputStatus()
xsDataResultStatusExpScreeningOutputLattices = xsDataResultISPyBExpected.getScreeningOutputLatticeStatus()
xsDataResultStatusExpScreeningStrategies = xsDataResultISPyBExpected.getScreeningStrategyStatus()
xsDataResultStatusExpScreeningStrategyWedges = xsDataResultISPyBExpected.getScreeningStrategyWedgeStatus()
xsDataResultStatusExpScreeningStrategySubWedges = xsDataResultISPyBExpected.getScreeningStrategySubWedgeStatus()
xsDataResultStatusExpScreeningRanks = xsDataResultISPyBExpected.getScreeningRankStatus()
xsDataResultStatusExpScreeningRankSet = xsDataResultISPyBExpected.getScreeningRankSetStatus()
xsDataIntegerDataCollectionId = xsDataResultISPyBObtained.getDataCollectionId()
xsDataResultStatusScreening = xsDataResultISPyBObtained.getScreeningStatus()
xsDataResultStatusScreeningInputs = xsDataResultISPyBObtained.getScreeningInputStatus()
xsDataResultStatusScreeningOutputs = xsDataResultISPyBObtained.getScreeningOutputStatus()
xsDataResultStatusScreeningOutputLattices = xsDataResultISPyBObtained.getScreeningOutputLatticeStatus()
xsDataResultStatusScreeningStrategies = xsDataResultISPyBObtained.getScreeningStrategyStatus()
xsDataResultStatusScreeningStrategyWedges = xsDataResultISPyBObtained.getScreeningStrategyWedgeStatus()
xsDataResultStatusScreeningStrategySubWedges = xsDataResultISPyBObtained.getScreeningStrategySubWedgeStatus()
xsDataResultStatusScreeningRanks = xsDataResultISPyBObtained.getScreeningRankStatus()
xsDataResultStatusScreeningRankSet = xsDataResultISPyBObtained.getScreeningRankSetStatus()
if xsDataIntegerExpDataCollectionId != None:
self.DEBUG("Checking dataCollectionId ...")
EDAssert.equal(xsDataIntegerDataCollectionId.getValue(), xsDataIntegerExpDataCollectionId.getValue())
if xsDataResultStatusExpScreening != None:
self.DEBUG("Checking screening ...")
EDAssert.equal(xsDataResultStatusScreening.getCode().getValue(), "ok")
iId = xsDataResultStatusScreening.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningInputs != None:
self.DEBUG("Checking inputs...")
for xsDataResultStatusScreeningInput in xsDataResultStatusScreeningInputs:
EDAssert.equal(xsDataResultStatusScreeningInput.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningInput.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningOutputs != None:
self.DEBUG("Checking outputs ...")
for xsDataResultStatusScreeningOutput in xsDataResultStatusScreeningOutputs:
EDAssert.equal(xsDataResultStatusScreeningOutput.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningOutput.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningOutputLattices != None:
self.DEBUG("Checking output lattices...")
for xsDataResultStatusScreeningOutputLattice in xsDataResultStatusScreeningOutputLattices:
EDAssert.equal(xsDataResultStatusScreeningOutputLattice.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningOutputLattice.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningStrategies != None:
self.DEBUG("Checking strategies...")
for xsDataResultStatusScreeningStrategy in xsDataResultStatusScreeningStrategies:
EDAssert.equal(xsDataResultStatusScreeningStrategy.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningStrategy.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningStrategyWedges != None:
self.DEBUG("Checking strategy wedges...")
for xsDataResultStatusScreeningStrategyWedge in xsDataResultStatusScreeningStrategyWedges:
EDAssert.equal(xsDataResultStatusScreeningStrategyWedge.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningStrategyWedge.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningStrategySubWedges != None:
self.DEBUG("Checking strategy subwedges...")
for xsDataResultStatusScreeningStrategySubWedge in xsDataResultStatusScreeningStrategySubWedges:
EDAssert.equal(xsDataResultStatusScreeningStrategySubWedge.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningStrategySubWedge.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusExpScreeningRanks != None:
self.DEBUG("Checking ranks...")
for xsDataResultStatusScreeningRank in xsDataResultStatusScreeningRanks:
EDAssert.equal(xsDataResultStatusScreeningRank.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningRank.getId().getValue()
EDAssert.equal((iId >= 0), True)
if xsDataResultStatusScreeningRankSet != None:
self.DEBUG("Checking rank sets...")
EDAssert.equal(xsDataResultStatusScreeningRankSet.getCode().getValue(), "ok")
iId = xsDataResultStatusScreeningRankSet.getId().getValue()
EDAssert.equal((iId >= 0), True)
class EDPluginISPyBv1_2(EDPluginExec):
"""
Plugin to store results in an ISPyB database using the DNA/ISPyB dbserver
"""
def __init__(self):
"""
Sets default values for dbserver parameters
"""
EDPluginExec.__init__(self)
self.setXSDataInputClass(XSDataISPyBScreening, "screening") # [0, 1]
self.setXSDataInputClass(XSDataISPyBScreeningInput,
"screeningInput") # [0, infinite]
self.setXSDataInputClass(XSDataISPyBScreeningOutputContainer,
"screeningOutputContainer") # [0, infinite]
self.setXSDataInputClass(XSDataISPyBScreeningRank,
"screeningRank") # [0, infinite]
self.setXSDataInputClass(XSDataISPyBScreeningRankSet,
"screeningRankSet") # [0, 1]
self.setXSDataInputClass(XSDataISPyBScreeningFile,
"screeningFile") # [0, infinite]
self.setXSDataInputClass(XSDataISPyBImage, "image") # [0, 1]
self.__strDbserverHost = "localhost"
self.__iDbserverPort = 9090
def getDbserverHost(self):
return self.__strDbserverHost
def setDbserverHost(self, _strDbserverHost):
self.__strDbserverHost = _strDbserverHost
def getDbserverPort(self):
return self.__iDbserverPort
def setDbserverPort(self, _iDbserverPort):
self.__iDbserverPort = _iDbserverPort
def configure(self):
"""
Gets the dbserver parameters from the config file and stores them in class member attributes.
"""
EDPluginExec.configure(self)
pluginConfiguration = self.getConfiguration()
if (pluginConfiguration == None):
self.DEBUG(
"*** EDPluginISPyBv1_2.configure: pluginConfiguration is None, using default settings"
)
else:
self.DEBUG(
"*** EDPluginISPyBv1_2.configure: pluginConfiguration found, using settings from there"
)
strDbserverHost = EDConfiguration.getStringParamValue(
pluginConfiguration, "dbserverHost")
if (strDbserverHost == None):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2.configure", self.getClassName(), \
"Configuration parameter missing: dbserverHost")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.setDbserverHost(strDbserverHost)
strDbserverPort = EDConfiguration.getStringParamValue(
pluginConfiguration, "dbserverPort")
if (strDbserverPort == None):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2.configure", self.getClassName(), \
"Configuration parameter missing: dbserverPort")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
self.setDbserverPort(int(strDbserverPort))
def process(self, _edObject=None):
"""
Sends store requests with the screening objects to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput("inputISPyB")[0] will be stored.
* Primary key attributes should not be set.
* If a foreign key attribute is not set, this method will attempt to find the foreign object among the
input objects, and then use the primary key attribute of this object when it has been stored. If such
an object is not found, the method fails.
* If an error is encountered, the method will immediately fail and will not attempt to store any more
objects.
"""
EDPluginExec.process(self)
self.DEBUG("*** EDPluginISPyBv1_2.process")
# Basic sanity check of inputs:
if (self.hasDataInput("screening")):
if (len(self.getDataInput("screening")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process",
"There should only be one input 'screening'.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if (self.hasDataInput("screeningRankSet")):
if (len(self.getDataInput("screeningRankSet")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process",
"There should only be one input 'screeningRankSet'.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Get the inputs
xsDataISPyBScreenings = None
xsDataISPyBScreeningInputs = None
xsDataISPyBScreeningOutputContainers = None
xsDataISPyBScreeningRanks = None
xsDataISPyBScreeningRankSets = None
xsDataISPyBImages = None
xsDataISPyBScreeningFiles = None
if self.hasDataInput("screening"):
xsDataISPyBScreenings = self.getDataInput("screening")
if self.hasDataInput("screeningInput"):
xsDataISPyBScreeningInputs = self.getDataInput("screeningInput")
if self.hasDataInput("screeningOutputContainer"):
xsDataISPyBScreeningOutputContainers = self.getDataInput(
"screeningOutputContainer")
if self.hasDataInput("screeningRank"):
xsDataISPyBScreeningRanks = self.getDataInput("screeningRank")
if self.hasDataInput("screeningRankSet"):
xsDataISPyBScreeningRankSets = self.getDataInput(
"screeningRankSet")
if self.hasDataInput("image"):
xsDataISPyBImages = self.getDataInput("image")
if self.hasDataInput("screeningFile"):
xsDataISPyBScreeningFiles = self.getDataInput("screeningFile")
self.__xsDataResultISPyB = XSDataResultISPyB()
if (xsDataISPyBScreenings is None):
xsDataISPyBScreening = XSDataISPyBScreening()
else:
xsDataISPyBScreening = xsDataISPyBScreenings[0]
if (xsDataISPyBImages is None):
xsDataISPyBImage = None
else:
xsDataISPyBImage = xsDataISPyBImages[0]
# Another sanity check:
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None)
or (xsDataISPyBImage.getFileName() == None)
or (xsDataISPyBImage.getFileLocation() == None)):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", \
"Neither a dataCollectionId nor an image filename + path are provided.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
strResponse = self.httpPost(self.getDbserverHost(),
self.getDbserverPort(),
"/get_datacollectionid", strXML)
if strResponse != None:
# Handle response:
xsDatadbstatus = XSDatadbstatus.parseString(strResponse)
strCode = xsDatadbstatus.getCode()
strMessage = xsDatadbstatus.getMessage()
self.DEBUG("dbserver returns code: " + strCode)
self.DEBUG("dbserver returns message: " + strMessage)
if (strCode
== "error") or (xsDatadbstatus.getDataCollectionId()
== -1):
if xsDatadbstatus.getDataCollectionId() == -1:
strMessage = "An image corresponding to the given fileName and fileLocation was not found."
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process", strMessage)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(
XSDataInteger(xsDatadbstatus.getDataCollectionId()))
self.__xsDataResultISPyB.setDataCollectionId(
XSDataInteger(xsDatadbstatus.getDataCollectionId()))
if (xsDataISPyBScreeningRankSets is None):
xsDataISPyBScreeningRankSet = None
else:
xsDataISPyBScreeningRankSet = xsDataISPyBScreeningRankSets[0]
# Store all the different screening* objects:
xsDataIntegerScreeningId = self.store(xsDataISPyBScreening)
if xsDataISPyBScreeningInputs != None:
for xsDataISPyBScreeningInput in xsDataISPyBScreeningInputs:
xsDataISPyBScreeningInput.setScreeningId(
xsDataIntegerScreeningId)
self.store(xsDataISPyBScreeningInput)
if xsDataISPyBScreeningRankSet != None:
xsDataIntegerScreeningRankSetId = self.store(
xsDataISPyBScreeningRankSet)
for xsDataISPyBScreeningRank in xsDataISPyBScreeningRanks:
xsDataISPyBScreeningRank.setScreeningId(
xsDataIntegerScreeningId)
xsDataISPyBScreeningRank.setScreeningRankSetId(
xsDataIntegerScreeningRankSetId)
self.store(xsDataISPyBScreeningRank)
if xsDataISPyBScreeningOutputContainers != None:
for xsDataISPyBScreeningOutputContainer in xsDataISPyBScreeningOutputContainers:
xsDataISPyBScreeningOutput = xsDataISPyBScreeningOutputContainer.getScreeningOutput(
)
xsDataISPyBScreeningOutput.setScreeningId(
xsDataIntegerScreeningId)
xsDataIntegerScreeningOutputId = self.store(
xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputLattices = xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice(
)
if xsDataISPyBScreeningOutputLattices != None:
for xsDataISPyBScreeningOutputLattice in xsDataISPyBScreeningOutputLattices:
xsDataISPyBScreeningOutputLattice.setScreeningOutputId(
xsDataIntegerScreeningOutputId)
self.store(xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningStrategyContainers = xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer(
)
if xsDataISPyBScreeningStrategyContainers != None:
for xsDataISPyBScreeningStrategyContainer in xsDataISPyBScreeningStrategyContainers:
xsDataISPyBScreeningStrategy = xsDataISPyBScreeningStrategyContainer.getScreeningStrategy(
)
if xsDataISPyBScreeningStrategy != None:
xsDataISPyBScreeningStrategy.setScreeningOutputId(
xsDataIntegerScreeningOutputId)
xsDataIntegerScreeningStrategyId = self.store(
xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningStrategyWedgeContainers = xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer(
)
if xsDataISPyBScreeningStrategyWedgeContainers != None:
for xsDataISPyBScreeningStrategyWedgeContainer in xsDataISPyBScreeningStrategyWedgeContainers:
xsDataISPyBScreeningStrategyWedge = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategyWedge(
)
xsDataISPyBScreeningStrategyWedge.setScreeningStrategyId(
xsDataIntegerScreeningStrategyId)
xsDataIntegerScreeningStrategyWedgeId = self.store(
xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategySubWedges = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge(
)
if xsDataISPyBScreeningStrategySubWedges != None:
for xsDataISPyBScreeningStrategySubWedge in xsDataISPyBScreeningStrategySubWedges:
xsDataISPyBScreeningStrategySubWedge.setScreeningStrategyWedgeId(
xsDataIntegerScreeningStrategyWedgeId
)
self.store(
xsDataISPyBScreeningStrategySubWedge
)
def postProcess(self, _edObject=None):
"""
"""
EDPluginExec.postProcess(self)
self.DEBUG("*** EDPluginISPyBv1_2.postProcess")
if (self.__xsDataResultISPyB is not None):
self.setDataOutput(self.__xsDataResultISPyB)
def httpPost(self, _strHost, _iPort, _strPath, _strXML):
"""
Sends XML to the dbserver on the specified host and port with the specified path.
Returns the response XML from the dbserver.
@param _strHost: the host name for the dbserver
@type _strHost: string
@param _iPort: the port for the dbserver
@type _iPort: integer
@param _strPath: the path name for the request
@type _strPath: string
@param _strXML: the XML for the request
@type _strXML: string
"""
strData = None
try:
pyHTTPConnection = httplib.HTTPConnection(_strHost, _iPort)
pyHTTPConnection.putrequest("POST", _strPath)
pyHTTPConnection.putheader("Content-type", "text/xml")
pyHTTPConnection.putheader("Content-length", "%d" % len(_strXML))
pyHTTPConnection.putheader('Accept', 'text/plain')
if "HOSTNAME" in os.environ.keys():
pyHTTPConnection.putheader('Host', os.environ["HOSTNAME"])
pyHTTPConnection.endheaders()
pyHTTPConnection.send(_strXML)
pyHTTPResponse = pyHTTPConnection.getresponse()
strMsg = pyHTTPResponse.msg
strHeaders = pyHTTPResponse.getheaders()
strReply = str(
pyHTTPResponse.status) + ' - ' + pyHTTPResponse.reason
strContentLength = pyHTTPResponse.getheader("Content-Length")
if strContentLength is None:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "httpPost", \
"No header returned for %s, host %s, port %d. HTTP resonse was: %s" \
% (_strPath, _strHost, _iPort, strReply))
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
try:
ilength = string.atoi(strContentLength)
except:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "httpPost", \
"Cannot convert Content-Length %s to integer for %s, host %s, port %d!" \
% (strContentLength, _strPath, _strHost, _iPort))
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
strData = pyHTTPResponse.read()
except (socket.error, httplib.BadStatusLine), (msg):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "httpPost", \
"Have you set up a connection to the dbserver? Error is: %s" % (msg))
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
raise RuntimeError, strErrorMessage
return strData
def process(self, _edObject=None):
"""
Sends store requests with the screening objects to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput("inputISPyB")[0] will be stored.
* Primary key attributes should not be set.
* If a foreign key attribute is not set, this method will attempt to find the foreign object among the
input objects, and then use the primary key attribute of this object when it has been stored. If such
an object is not found, the method fails.
* If an error is encountered, the method will immediately fail and will not attempt to store any more
objects.
"""
EDPluginExec.process(self)
self.DEBUG("*** EDPluginISPyBv1_2.process")
# Basic sanity check of inputs:
if (self.hasDataInput("screening")):
if (len(self.getDataInput("screening")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process",
"There should only be one input 'screening'.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
if (self.hasDataInput("screeningRankSet")):
if (len(self.getDataInput("screeningRankSet")) > 1):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process",
"There should only be one input 'screeningRankSet'.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Get the inputs
xsDataISPyBScreenings = None
xsDataISPyBScreeningInputs = None
xsDataISPyBScreeningOutputContainers = None
xsDataISPyBScreeningRanks = None
xsDataISPyBScreeningRankSets = None
xsDataISPyBImages = None
xsDataISPyBScreeningFiles = None
if self.hasDataInput("screening"):
xsDataISPyBScreenings = self.getDataInput("screening")
if self.hasDataInput("screeningInput"):
xsDataISPyBScreeningInputs = self.getDataInput("screeningInput")
if self.hasDataInput("screeningOutputContainer"):
xsDataISPyBScreeningOutputContainers = self.getDataInput(
"screeningOutputContainer")
if self.hasDataInput("screeningRank"):
xsDataISPyBScreeningRanks = self.getDataInput("screeningRank")
if self.hasDataInput("screeningRankSet"):
xsDataISPyBScreeningRankSets = self.getDataInput(
"screeningRankSet")
if self.hasDataInput("image"):
xsDataISPyBImages = self.getDataInput("image")
if self.hasDataInput("screeningFile"):
xsDataISPyBScreeningFiles = self.getDataInput("screeningFile")
self.__xsDataResultISPyB = XSDataResultISPyB()
if (xsDataISPyBScreenings is None):
xsDataISPyBScreening = XSDataISPyBScreening()
else:
xsDataISPyBScreening = xsDataISPyBScreenings[0]
if (xsDataISPyBImages is None):
xsDataISPyBImage = None
else:
xsDataISPyBImage = xsDataISPyBImages[0]
# Another sanity check:
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None)
or (xsDataISPyBImage.getFileName() == None)
or (xsDataISPyBImage.getFileLocation() == None)):
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv1_2", "process", \
"Neither a dataCollectionId nor an image filename + path are provided.")
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
strResponse = self.httpPost(self.getDbserverHost(),
self.getDbserverPort(),
"/get_datacollectionid", strXML)
if strResponse != None:
# Handle response:
xsDatadbstatus = XSDatadbstatus.parseString(strResponse)
strCode = xsDatadbstatus.getCode()
strMessage = xsDatadbstatus.getMessage()
self.DEBUG("dbserver returns code: " + strCode)
self.DEBUG("dbserver returns message: " + strMessage)
if (strCode
== "error") or (xsDatadbstatus.getDataCollectionId()
== -1):
if xsDatadbstatus.getDataCollectionId() == -1:
strMessage = "An image corresponding to the given fileName and fileLocation was not found."
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv1_2", "process", strMessage)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(
XSDataInteger(xsDatadbstatus.getDataCollectionId()))
self.__xsDataResultISPyB.setDataCollectionId(
XSDataInteger(xsDatadbstatus.getDataCollectionId()))
if (xsDataISPyBScreeningRankSets is None):
xsDataISPyBScreeningRankSet = None
else:
xsDataISPyBScreeningRankSet = xsDataISPyBScreeningRankSets[0]
# Store all the different screening* objects:
xsDataIntegerScreeningId = self.store(xsDataISPyBScreening)
if xsDataISPyBScreeningInputs != None:
for xsDataISPyBScreeningInput in xsDataISPyBScreeningInputs:
xsDataISPyBScreeningInput.setScreeningId(
xsDataIntegerScreeningId)
self.store(xsDataISPyBScreeningInput)
if xsDataISPyBScreeningRankSet != None:
xsDataIntegerScreeningRankSetId = self.store(
xsDataISPyBScreeningRankSet)
for xsDataISPyBScreeningRank in xsDataISPyBScreeningRanks:
xsDataISPyBScreeningRank.setScreeningId(
xsDataIntegerScreeningId)
xsDataISPyBScreeningRank.setScreeningRankSetId(
xsDataIntegerScreeningRankSetId)
self.store(xsDataISPyBScreeningRank)
if xsDataISPyBScreeningOutputContainers != None:
for xsDataISPyBScreeningOutputContainer in xsDataISPyBScreeningOutputContainers:
xsDataISPyBScreeningOutput = xsDataISPyBScreeningOutputContainer.getScreeningOutput(
)
xsDataISPyBScreeningOutput.setScreeningId(
xsDataIntegerScreeningId)
xsDataIntegerScreeningOutputId = self.store(
xsDataISPyBScreeningOutput)
xsDataISPyBScreeningOutputLattices = xsDataISPyBScreeningOutputContainer.getScreeningOutputLattice(
)
if xsDataISPyBScreeningOutputLattices != None:
for xsDataISPyBScreeningOutputLattice in xsDataISPyBScreeningOutputLattices:
xsDataISPyBScreeningOutputLattice.setScreeningOutputId(
xsDataIntegerScreeningOutputId)
self.store(xsDataISPyBScreeningOutputLattice)
xsDataISPyBScreeningStrategyContainers = xsDataISPyBScreeningOutputContainer.getScreeningStrategyContainer(
)
if xsDataISPyBScreeningStrategyContainers != None:
for xsDataISPyBScreeningStrategyContainer in xsDataISPyBScreeningStrategyContainers:
xsDataISPyBScreeningStrategy = xsDataISPyBScreeningStrategyContainer.getScreeningStrategy(
)
if xsDataISPyBScreeningStrategy != None:
xsDataISPyBScreeningStrategy.setScreeningOutputId(
xsDataIntegerScreeningOutputId)
xsDataIntegerScreeningStrategyId = self.store(
xsDataISPyBScreeningStrategy)
xsDataISPyBScreeningStrategyWedgeContainers = xsDataISPyBScreeningStrategyContainer.getScreeningStrategyWedgeContainer(
)
if xsDataISPyBScreeningStrategyWedgeContainers != None:
for xsDataISPyBScreeningStrategyWedgeContainer in xsDataISPyBScreeningStrategyWedgeContainers:
xsDataISPyBScreeningStrategyWedge = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategyWedge(
)
xsDataISPyBScreeningStrategyWedge.setScreeningStrategyId(
xsDataIntegerScreeningStrategyId)
xsDataIntegerScreeningStrategyWedgeId = self.store(
xsDataISPyBScreeningStrategyWedge)
xsDataISPyBScreeningStrategySubWedges = xsDataISPyBScreeningStrategyWedgeContainer.getScreeningStrategySubWedge(
)
if xsDataISPyBScreeningStrategySubWedges != None:
for xsDataISPyBScreeningStrategySubWedge in xsDataISPyBScreeningStrategySubWedges:
xsDataISPyBScreeningStrategySubWedge.setScreeningStrategyWedgeId(
xsDataIntegerScreeningStrategyWedgeId
)
self.store(
xsDataISPyBScreeningStrategySubWedge
)
