def testExecute(self):
"""
Runs the plugin and then compares expected output with obtained output to verify that it executed correctly.
"""
self.run()
# Checks the expected result
strExpectedOutput = self.readAndParseFile (self.getReferenceDataOutputFile())
strObtainedOutput = self.readAndParseFile(self.m_edObtainedOutputDataFile)
xsDataResultISPyBObtained = XSDataResultISPyB.parseString(strObtainedOutput)
xsDataResultStatusListObtained = xsDataResultISPyBObtained.getResultStatus()
EDVerbose.DEBUG("Checking obtained result...")
for xsDataResultStatusObtained in xsDataResultStatusListObtained:
EDAssert.equal(xsDataResultStatusObtained.getCode().getValue(), "ok")
class EDPluginISPyBv10(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(XSDataInputISPyB)
self.__strDbserverHost = "localhost"
self.m_iDbserverPort = 9090
def getDbserverHost(self):
return self.__strDbserverHost
def setDbserverHost(self, _strDbserverHost):
self.__strDbserverHost = _strDbserverHost
def getDbserverPort(self):
return self.m_iDbserverPort
def setDbserverPort(self, _iDbserverPort):
self.m_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(
"*** EDPluginISPyBv10.configure: pluginConfiguration is None, using default settings"
)
else:
self.DEBUG(
"*** EDPluginISPyBv10.configure: pluginConfiguration found, using settings from there"
)
pyStrDbserverHost = EDConfiguration.getStringParamValue(
pluginConfiguration, "dbserverHost")
if (pyStrDbserverHost == None):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10.configure", self.getClassName(), \
"Configuration parameter missing: dbserverHost")
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
else:
self.setDbserverHost(pyStrDbserverHost)
pyStrDbserverPort = EDConfiguration.getStringParamValue(
pluginConfiguration, "dbserverPort")
if (pyStrDbserverPort == None):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10.configure", self.getClassName(), \
"Configuration parameter missing: dbserverPort")
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
else:
self.setDbserverPort(int(pyStrDbserverPort))
def process(self, _edObject=None):
"""
Sends a store request and the screening object to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput() 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 those
referred to by the self.getDataInput() object, and use the primary key attribute of this object when it
has been stored. If such an object is not found, the method fails.
* The method will not attempt to store any more objects once an error is encountered
"""
EDPluginExec.process(self)
self.DEBUG("*** EDPluginISPyBv10.process")
xsDataInputISPyB = self.getDataInput()
self.m_xsDataResultISPyB = XSDataResultISPyB()
xsDataISPyBScreening = xsDataInputISPyB.getScreening()
if xsDataISPyBScreening == None:
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBImage = xsDataInputISPyB.getImage()
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None)
or (xsDataISPyBImage.getFileName() == None)
or (xsDataISPyBImage.getFileLocation() == None)):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "process", \
"Neither a dataCollectionId nor a image filename + path are provided.")
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
edStringResponse = self.httpPost(self.getDbserverHost(),
self.getDbserverPort(),
"/get_datacollectionid", strXML)
if edStringResponse != None:
# Handle response:
self.DEBUG(edStringResponse)
xsDatadbstatus = XSDatadbstatus.parseString(edStringResponse)
pyStrCode = xsDatadbstatus.getCode()
pyStrMessage = xsDatadbstatus.getMessage()
self.DEBUG("dbserver returns code: " + pyStrCode)
self.DEBUG("dbserver returns message: " + pyStrMessage)
if (pyStrCode
== "error") or (xsDatadbstatus.getDataCollectionId()
== -1):
if xsDatadbstatus.getDataCollectionId() == -1:
pyStrMessage = "An image corresponding to the given fileName and fileLocation was not found."
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv10", "process", pyStrMessage)
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(
XSDataInteger(xsDatadbstatus.getDataCollectionId()))
self.DEBUG("dataCollectionId is: " + str(
xsDataISPyBScreening.getDataCollectionId().getValue()))
xsDataISPyBScreeningInput = xsDataInputISPyB.getScreeningInput()
xsDataISPyBScreeningOutput = xsDataInputISPyB.getScreeningOutput()
xsDataISPyBScreeningOutputLattice = xsDataInputISPyB.getScreeningOutputLattice(
)
xsDataISPyBScreeningRank = xsDataInputISPyB.getScreeningRank()
xsDataISPyBScreeningRankSet = xsDataInputISPyB.getScreeningRankSet()
xsDataISPyBScreeningStrategy = xsDataInputISPyB.getScreeningStrategy()
for xsDataISPyBScreeningObject in [ xsDataISPyBScreening, xsDataISPyBScreeningRankSet, xsDataISPyBScreeningInput, xsDataISPyBScreeningOutput, \
xsDataISPyBScreeningOutputLattice, xsDataISPyBScreeningRank, xsDataISPyBScreeningStrategy ]:
if xsDataISPyBScreeningObject != None:
# Set any missing foreign key attributes in xsDataScreeningObject:
self.setForeignKeyAttributes(xsDataISPyBScreeningObject,
self.m_xsDataResultISPyB)
# Create DNA compatible XML from xsDataScreeningObject:
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBScreeningObject)
# Send the XML to the dbserver:
edStringResponse = self.httpPost(self.getDbserverHost(),
self.getDbserverPort(),
"/store_object_request",
strXML)
if edStringResponse != None:
# Handle response:
self.DEBUG(edStringResponse)
xsDatadbstatus = XSDatadbstatus.parseString(
edStringResponse)
pyStrCode = xsDatadbstatus.getCode()
pyStrMessage = xsDatadbstatus.getMessage()
xsDataStrCode = XSDataString(pyStrCode)
xsDataStrMessage = XSDataString(pyStrMessage)
self.DEBUG("dbserver returns code: " + pyStrCode)
self.DEBUG("dbserver returns message: " + pyStrMessage)
xsDataResultStatusList = self.m_xsDataResultISPyB.getResultStatus(
)
xsDataResultStatus = XSDataResultStatus(
xsDataISPyBScreeningObject, xsDataStrCode,
xsDataStrMessage)
xsDataResultStatusList.append(xsDataResultStatus)
self.addToXSDataResultISPyB(self.m_xsDataResultISPyB,
xsDatadbstatus)
if pyStrCode == "error":
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv10", "process", pyStrMessage)
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
else:
return
def postProcess(self, _edObject=None):
"""
"""
EDPluginExec.postProcess(self)
self.DEBUG("*** EDPluginISPyBv10.postProcess")
if (self.m_xsDataResultISPyB is not None):
self.setDataOutput(self.m_xsDataResultISPyB)
xsDataResultStatusList = self.m_xsDataResultISPyB.getResultStatus()
for xsDataResultStatus in xsDataResultStatusList:
xsDataObject = xsDataResultStatus.getScreeningObject()
xsDataStrCode = xsDataResultStatus.getCode()
xsDataStrMessage = xsDataResultStatus.getMessage()
if xsDataStrCode.getValue() == "error":
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "postProcess", "Could not store object of class %s." \
% xsDataObject.__class__.__name__)
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
if len(xsDataResultStatusList) == 0:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv10", "postProcess", "No objects stored.")
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
def setForeignKeyAttributes(self, _xsDataISPyBScreeningObject,
_xsDataResultISPyB):
"""
Sets missing foreign key attributes in _xsDataISPyBScreeningObject if available
"""
className = _xsDataISPyBScreeningObject.__class__.__name__
# Set required foreign key attributes:
if className in [
"XSDataISPyBScreeningInput", "XSDataISPyBScreeningOutput",
"XSDataISPyBScreeningRank"
]:
if _xsDataISPyBScreeningObject.getScreeningId() == None:
xsDataInteger = _xsDataResultISPyB.getScreeningId()
_xsDataISPyBScreeningObject.setScreeningId(xsDataInteger)
if className == "XSDataISPyBScreeningRank":
if _xsDataISPyBScreeningObject.getScreeningRankId() == None:
xsDataInteger = _xsDataResultISPyB.getScreeningRankId()
_xsDataISPyBScreeningObject.setScreeningRankId(xsDataInteger)
if className in [
"XSDataISPyBScreeningStrategy",
"XSDataISPyBScreeningOutputLattice"
]:
if _xsDataISPyBScreeningObject.getScreeningOutputId() == None:
xsDataInteger = _xsDataResultISPyB.getScreeningOutputId()
_xsDataISPyBScreeningObject.setScreeningOutputId(xsDataInteger)
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.
"""
try:
pyHTTPConnection = PyHttplib.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 PyOs.environ.keys():
pyHTTPConnection.putheader('Host', PyOs.environ["HOSTNAME"])
pyHTTPConnection.endheaders()
pyHTTPConnection.send(_strXML)
pyHTTPResponse = pyHTTPConnection.getresponse()
pyStrMsg = pyHTTPResponse.msg
pyStrHeaders = pyHTTPResponse.getheaders()
pyStrReply = str(
pyHTTPResponse.status) + ' - ' + pyHTTPResponse.reason
pyStrContentLength = pyHTTPResponse.getheader("Content-Length")
if pyStrContentLength is None:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "httpPost", \
"No header returned for %s, host %s, port %d. HTTP resonse was: %s" \
% (_strPath, _strHost, _iPort, pyStrReply))
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
try:
ilength = PyString.atoi(pyStrContentLength)
except:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "httpPost", \
"Cannot convert Content-Length %s to integer for %s, host %s, port %d!" \
% (pyStrContentLength, _strPath, _strHost, _iPort))
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
pyStrData = pyHTTPResponse.read()
except (PySocket.error, PyHttplib.BadStatusLine), (msg):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "httpPost", \
"Have you set up a connection to the dbserver? Error is: %s" % (msg))
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return None
return pyStrData
def process(self, _edObject=None):
"""
Sends a store request and the screening object to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput() 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 those
referred to by the self.getDataInput() object, and use the primary key attribute of this object when it
has been stored. If such an object is not found, the method fails.
* The method will not attempt to store any more objects once an error is encountered
"""
EDPluginExec.process(self)
self.DEBUG("*** EDPluginISPyBv10.process")
xsDataInputISPyB = self.getDataInput()
self.m_xsDataResultISPyB = XSDataResultISPyB()
xsDataISPyBScreening = xsDataInputISPyB.getScreening()
if xsDataISPyBScreening == None:
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBImage = xsDataInputISPyB.getImage()
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None)
or (xsDataISPyBImage.getFileName() == None)
or (xsDataISPyBImage.getFileLocation() == None)):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "process", \
"Neither a dataCollectionId nor a image filename + path are provided.")
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
edStringResponse = self.httpPost(self.getDbserverHost(),
self.getDbserverPort(),
"/get_datacollectionid", strXML)
if edStringResponse != None:
# Handle response:
self.DEBUG(edStringResponse)
xsDatadbstatus = XSDatadbstatus.parseString(edStringResponse)
pyStrCode = xsDatadbstatus.getCode()
pyStrMessage = xsDatadbstatus.getMessage()
self.DEBUG("dbserver returns code: " + pyStrCode)
self.DEBUG("dbserver returns message: " + pyStrMessage)
if (pyStrCode
== "error") or (xsDatadbstatus.getDataCollectionId()
== -1):
if xsDatadbstatus.getDataCollectionId() == -1:
pyStrMessage = "An image corresponding to the given fileName and fileLocation was not found."
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv10", "process", pyStrMessage)
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(
XSDataInteger(xsDatadbstatus.getDataCollectionId()))
self.DEBUG("dataCollectionId is: " + str(
xsDataISPyBScreening.getDataCollectionId().getValue()))
xsDataISPyBScreeningInput = xsDataInputISPyB.getScreeningInput()
xsDataISPyBScreeningOutput = xsDataInputISPyB.getScreeningOutput()
xsDataISPyBScreeningOutputLattice = xsDataInputISPyB.getScreeningOutputLattice(
)
xsDataISPyBScreeningRank = xsDataInputISPyB.getScreeningRank()
xsDataISPyBScreeningRankSet = xsDataInputISPyB.getScreeningRankSet()
xsDataISPyBScreeningStrategy = xsDataInputISPyB.getScreeningStrategy()
for xsDataISPyBScreeningObject in [ xsDataISPyBScreening, xsDataISPyBScreeningRankSet, xsDataISPyBScreeningInput, xsDataISPyBScreeningOutput, \
xsDataISPyBScreeningOutputLattice, xsDataISPyBScreeningRank, xsDataISPyBScreeningStrategy ]:
if xsDataISPyBScreeningObject != None:
# Set any missing foreign key attributes in xsDataScreeningObject:
self.setForeignKeyAttributes(xsDataISPyBScreeningObject,
self.m_xsDataResultISPyB)
# Create DNA compatible XML from xsDataScreeningObject:
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBScreeningObject)
# Send the XML to the dbserver:
edStringResponse = self.httpPost(self.getDbserverHost(),
self.getDbserverPort(),
"/store_object_request",
strXML)
if edStringResponse != None:
# Handle response:
self.DEBUG(edStringResponse)
xsDatadbstatus = XSDatadbstatus.parseString(
edStringResponse)
pyStrCode = xsDatadbstatus.getCode()
pyStrMessage = xsDatadbstatus.getMessage()
xsDataStrCode = XSDataString(pyStrCode)
xsDataStrMessage = XSDataString(pyStrMessage)
self.DEBUG("dbserver returns code: " + pyStrCode)
self.DEBUG("dbserver returns message: " + pyStrMessage)
xsDataResultStatusList = self.m_xsDataResultISPyB.getResultStatus(
)
xsDataResultStatus = XSDataResultStatus(
xsDataISPyBScreeningObject, xsDataStrCode,
xsDataStrMessage)
xsDataResultStatusList.append(xsDataResultStatus)
self.addToXSDataResultISPyB(self.m_xsDataResultISPyB,
xsDatadbstatus)
if pyStrCode == "error":
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
"EDPluginISPyBv10", "process", pyStrMessage)
self.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
else:
return
class EDPluginISPyBv10(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(XSDataInputISPyB)
self.__strDbserverHost = "localhost"
self.m_iDbserverPort = 9090
def getDbserverHost(self):
return self.__strDbserverHost
def setDbserverHost(self, _strDbserverHost):
self.__strDbserverHost = _strDbserverHost
def getDbserverPort(self):
return self.m_iDbserverPort
def setDbserverPort(self, _iDbserverPort):
self.m_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("*** EDPluginISPyBv10.configure: pluginConfiguration is None, using default settings")
else:
EDVerbose.DEBUG("*** EDPluginISPyBv10.configure: pluginConfiguration found, using settings from there")
pyStrDbserverHost = EDConfiguration.getStringParamValue(pluginConfiguration, "dbserverHost")
if(pyStrDbserverHost == None):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10.configure", self.getClassName(), \
"Configuration parameter missing: dbserverHost")
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
else:
self.setDbserverHost(pyStrDbserverHost)
pyStrDbserverPort = EDConfiguration.getStringParamValue(pluginConfiguration, "dbserverPort")
if(pyStrDbserverPort == None):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10.configure", self.getClassName(), \
"Configuration parameter missing: dbserverPort")
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
else:
self.setDbserverPort(int (pyStrDbserverPort))
def process(self, _edObject=None):
"""
Sends a store request and the screening object to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput() 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 those
referred to by the self.getDataInput() object, and use the primary key attribute of this object when it
has been stored. If such an object is not found, the method fails.
* The method will not attempt to store any more objects once an error is encountered
"""
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginISPyBv10.process")
xsDataInputISPyB = self.getDataInput()
self.m_xsDataResultISPyB = XSDataResultISPyB()
xsDataISPyBScreening = xsDataInputISPyB.getScreening()
if xsDataISPyBScreening == None:
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBImage = xsDataInputISPyB.getImage()
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None) or (xsDataISPyBImage.getFileName() == None) or (xsDataISPyBImage.getFileLocation() == None)):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "process", \
"Neither a dataCollectionId nor a image filename + path are provided.")
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
edStringResponse = self.httpPost(self.getDbserverHost(), self.getDbserverPort(), "/get_datacollectionid", strXML)
if edStringResponse != None:
# Handle response:
EDVerbose.DEBUG(edStringResponse)
xsDatadbstatus = XSDatadbstatus.parseString(edStringResponse)
pyStrCode = xsDatadbstatus.getCode()
pyStrMessage = xsDatadbstatus.getMessage()
EDVerbose.DEBUG("dbserver returns code: " + pyStrCode)
EDVerbose.DEBUG("dbserver returns message: " + pyStrMessage)
if (pyStrCode == "error") or (xsDatadbstatus.getDataCollectionId() == -1):
if xsDatadbstatus.getDataCollectionId() == -1:
pyStrMessage = "An image corresponding to the given fileName and fileLocation was not found."
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "process", pyStrMessage)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(XSDataInteger(xsDatadbstatus.getDataCollectionId()))
EDVerbose.DEBUG("dataCollectionId is: " + str(xsDataISPyBScreening.getDataCollectionId().getValue()))
xsDataISPyBScreeningInput = xsDataInputISPyB.getScreeningInput()
xsDataISPyBScreeningOutput = xsDataInputISPyB.getScreeningOutput()
xsDataISPyBScreeningOutputLattice = xsDataInputISPyB.getScreeningOutputLattice()
xsDataISPyBScreeningRank = xsDataInputISPyB.getScreeningRank()
xsDataISPyBScreeningRankSet = xsDataInputISPyB.getScreeningRankSet()
xsDataISPyBScreeningStrategy = xsDataInputISPyB.getScreeningStrategy()
for xsDataISPyBScreeningObject in [ xsDataISPyBScreening, xsDataISPyBScreeningRankSet, xsDataISPyBScreeningInput, xsDataISPyBScreeningOutput, \
xsDataISPyBScreeningOutputLattice, xsDataISPyBScreeningRank, xsDataISPyBScreeningStrategy ]:
if xsDataISPyBScreeningObject != None:
# Set any missing foreign key attributes in xsDataScreeningObject:
self.setForeignKeyAttributes(xsDataISPyBScreeningObject, self.m_xsDataResultISPyB)
# Create DNA compatible XML from xsDataScreeningObject:
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBScreeningObject)
# Send the XML to the dbserver:
edStringResponse = self.httpPost(self.getDbserverHost(), self.getDbserverPort(), "/store_object_request", strXML)
if edStringResponse != None:
# Handle response:
EDVerbose.DEBUG(edStringResponse)
xsDatadbstatus = XSDatadbstatus.parseString(edStringResponse)
pyStrCode = xsDatadbstatus.getCode()
pyStrMessage = xsDatadbstatus.getMessage()
xsDataStrCode = XSDataString(pyStrCode)
xsDataStrMessage = XSDataString(pyStrMessage)
EDVerbose.DEBUG("dbserver returns code: " + pyStrCode)
EDVerbose.DEBUG("dbserver returns message: " + pyStrMessage)
xsDataResultStatusList = self.m_xsDataResultISPyB.getResultStatus()
xsDataResultStatus = XSDataResultStatus(xsDataISPyBScreeningObject, xsDataStrCode, xsDataStrMessage)
xsDataResultStatusList.append(xsDataResultStatus)
self.addToXSDataResultISPyB(self.m_xsDataResultISPyB, xsDatadbstatus)
if pyStrCode == "error":
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "process", pyStrMessage)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
else:
return
def postProcess(self, _edObject=None):
"""
"""
EDPluginExec.postProcess(self)
EDVerbose.DEBUG("*** EDPluginISPyBv10.postProcess")
if (self.m_xsDataResultISPyB is not None):
self.setDataOutput(self.m_xsDataResultISPyB)
xsDataResultStatusList = self.m_xsDataResultISPyB.getResultStatus()
for xsDataResultStatus in xsDataResultStatusList:
xsDataObject = xsDataResultStatus.getScreeningObject()
xsDataStrCode = xsDataResultStatus.getCode()
xsDataStrMessage = xsDataResultStatus.getMessage()
if xsDataStrCode.getValue() == "error":
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "postProcess", "Could not store object of class %s." \
% xsDataObject.__class__.__name__)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
if len(xsDataResultStatusList) == 0:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "postProcess", "No objects stored.")
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
def setForeignKeyAttributes(self, _xsDataISPyBScreeningObject, _xsDataResultISPyB):
"""
Sets missing foreign key attributes in _xsDataISPyBScreeningObject if available
"""
className = _xsDataISPyBScreeningObject.__class__.__name__
# Set required foreign key attributes:
if className in ["XSDataISPyBScreeningInput", "XSDataISPyBScreeningOutput", "XSDataISPyBScreeningRank" ]:
if _xsDataISPyBScreeningObject.getScreeningId() == None:
xsDataInteger = _xsDataResultISPyB.getScreeningId()
_xsDataISPyBScreeningObject.setScreeningId(xsDataInteger)
if className == "XSDataISPyBScreeningRank":
if _xsDataISPyBScreeningObject.getScreeningRankId() == None:
xsDataInteger = _xsDataResultISPyB.getScreeningRankId()
_xsDataISPyBScreeningObject.setScreeningRankId(xsDataInteger)
if className in [ "XSDataISPyBScreeningStrategy", "XSDataISPyBScreeningOutputLattice" ]:
if _xsDataISPyBScreeningObject.getScreeningOutputId() == None:
xsDataInteger = _xsDataResultISPyB.getScreeningOutputId()
_xsDataISPyBScreeningObject.setScreeningOutputId(xsDataInteger)
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.
"""
try:
pyHTTPConnection = PyHttplib.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 PyOs.environ.keys():
pyHTTPConnection.putheader('Host', PyOs.environ["HOSTNAME"])
pyHTTPConnection.endheaders()
pyHTTPConnection.send(_strXML)
pyHTTPResponse = pyHTTPConnection.getresponse()
pyStrMsg = pyHTTPResponse.msg
pyStrHeaders = pyHTTPResponse.getheaders()
pyStrReply = str(pyHTTPResponse.status) + ' - ' + pyHTTPResponse.reason
pyStrContentLength = pyHTTPResponse.getheader("Content-Length")
if pyStrContentLength is None:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "httpPost", \
"No header returned for %s, host %s, port %d. HTTP resonse was: %s" \
% (_strPath, _strHost, _iPort, pyStrReply))
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
try:
ilength = PyString.atoi(pyStrContentLength)
except:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "httpPost", \
"Cannot convert Content-Length %s to integer for %s, host %s, port %d!" \
% (pyStrContentLength, _strPath, _strHost, _iPort))
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
raise RuntimeError, pyStrErrorMessage
pyStrData = pyHTTPResponse.read()
except (PySocket.error, PyHttplib.BadStatusLine), (msg):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "httpPost", \
"Have you set up a connection to the dbserver? Error is: %s" % (msg))
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return None
return pyStrData
def process(self, _edObject=None):
"""
Sends a store request and the screening object to the dbserver. Returns success or failure.
Note that:
* Any objects referred to by the object returned by self.getDataInput() 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 those
referred to by the self.getDataInput() object, and use the primary key attribute of this object when it
has been stored. If such an object is not found, the method fails.
* The method will not attempt to store any more objects once an error is encountered
"""
EDPluginExec.process(self)
EDVerbose.DEBUG("*** EDPluginISPyBv10.process")
xsDataInputISPyB = self.getDataInput()
self.m_xsDataResultISPyB = XSDataResultISPyB()
xsDataISPyBScreening = xsDataInputISPyB.getScreening()
if xsDataISPyBScreening == None:
xsDataISPyBScreening = XSDataISPyBScreening()
xsDataISPyBImage = xsDataInputISPyB.getImage()
if xsDataISPyBScreening.getDataCollectionId() == None:
if ((xsDataISPyBImage == None) or (xsDataISPyBImage.getFileName() == None) or (xsDataISPyBImage.getFileLocation() == None)):
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "process", \
"Neither a dataCollectionId nor a image filename + path are provided.")
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBImage)
# Send the XML to request the dataCollectionId from the dbserver:
edStringResponse = self.httpPost(self.getDbserverHost(), self.getDbserverPort(), "/get_datacollectionid", strXML)
if edStringResponse != None:
# Handle response:
EDVerbose.DEBUG(edStringResponse)
xsDatadbstatus = XSDatadbstatus.parseString(edStringResponse)
pyStrCode = xsDatadbstatus.getCode()
pyStrMessage = xsDatadbstatus.getMessage()
EDVerbose.DEBUG("dbserver returns code: " + pyStrCode)
EDVerbose.DEBUG("dbserver returns message: " + pyStrMessage)
if (pyStrCode == "error") or (xsDatadbstatus.getDataCollectionId() == -1):
if xsDatadbstatus.getDataCollectionId() == -1:
pyStrMessage = "An image corresponding to the given fileName and fileLocation was not found."
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "process", pyStrMessage)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
if xsDatadbstatus.getDataCollectionId() != -1:
xsDataISPyBScreening.setDataCollectionId(XSDataInteger(xsDatadbstatus.getDataCollectionId()))
EDVerbose.DEBUG("dataCollectionId is: " + str(xsDataISPyBScreening.getDataCollectionId().getValue()))
xsDataISPyBScreeningInput = xsDataInputISPyB.getScreeningInput()
xsDataISPyBScreeningOutput = xsDataInputISPyB.getScreeningOutput()
xsDataISPyBScreeningOutputLattice = xsDataInputISPyB.getScreeningOutputLattice()
xsDataISPyBScreeningRank = xsDataInputISPyB.getScreeningRank()
xsDataISPyBScreeningRankSet = xsDataInputISPyB.getScreeningRankSet()
xsDataISPyBScreeningStrategy = xsDataInputISPyB.getScreeningStrategy()
for xsDataISPyBScreeningObject in [ xsDataISPyBScreening, xsDataISPyBScreeningRankSet, xsDataISPyBScreeningInput, xsDataISPyBScreeningOutput, \
xsDataISPyBScreeningOutputLattice, xsDataISPyBScreeningRank, xsDataISPyBScreeningStrategy ]:
if xsDataISPyBScreeningObject != None:
# Set any missing foreign key attributes in xsDataScreeningObject:
self.setForeignKeyAttributes(xsDataISPyBScreeningObject, self.m_xsDataResultISPyB)
# Create DNA compatible XML from xsDataScreeningObject:
strXML = EDUtilsXML.dnaMarshal(xsDataISPyBScreeningObject)
# Send the XML to the dbserver:
edStringResponse = self.httpPost(self.getDbserverHost(), self.getDbserverPort(), "/store_object_request", strXML)
if edStringResponse != None:
# Handle response:
EDVerbose.DEBUG(edStringResponse)
xsDatadbstatus = XSDatadbstatus.parseString(edStringResponse)
pyStrCode = xsDatadbstatus.getCode()
pyStrMessage = xsDatadbstatus.getMessage()
xsDataStrCode = XSDataString(pyStrCode)
xsDataStrMessage = XSDataString(pyStrMessage)
EDVerbose.DEBUG("dbserver returns code: " + pyStrCode)
EDVerbose.DEBUG("dbserver returns message: " + pyStrMessage)
xsDataResultStatusList = self.m_xsDataResultISPyB.getResultStatus()
xsDataResultStatus = XSDataResultStatus(xsDataISPyBScreeningObject, xsDataStrCode, xsDataStrMessage)
xsDataResultStatusList.append(xsDataResultStatus)
self.addToXSDataResultISPyB(self.m_xsDataResultISPyB, xsDatadbstatus)
if pyStrCode == "error":
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % ("EDPluginISPyBv10", "process", pyStrMessage)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
return
else:
return