def finallyProcess(self, _edPlugin=None):
EDPluginExec.finallyProcess(self, _edPlugin)
self.DEBUG("EDPluginExecSimpleHTMLPagev1_1.finallyProcess...")
xsDataResultSimpleHTMLPage = XSDataResultSimpleHTMLPage()
xsDataResultSimpleHTMLPage.setPathToHTMLFile(XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.strHtmlFileName))))
xsDataResultSimpleHTMLPage.setPathToHTMLDirectory(XSDataFile(XSDataString(self.getWorkingDirectory())))
# Write workflowStepReport HTML page
pathToIndexFile = self.workflowStepReport.renderHtml(self.getWorkingDirectory(), nameOfIndexFile=self.strHtmlFileName)
pathToJsonFile = self.workflowStepReport.renderJson(self.getWorkingDirectory())
# Store in Pyarch
if EDUtilsPath.isESRF() or EDUtilsPath.isEMBL() or EDUtilsPath.isMAXIV() or EDUtilsPath.isALBA:
strPyarchPath = None
if self.xsDataResultCharacterisation is not None:
strPyarchPath = EDHandlerESRFPyarchv1_0.createPyarchHtmlDirectoryPath(self.xsDataResultCharacterisation.getDataCollection())
if strPyarchPath is None:
# For debugging purposes
strPyarchPath = EDUtilsPath.getEdnaUserTempFolder()
EDHandlerESRFPyarchv1_0.copyHTMLDir(_strPathToHTMLDir=os.path.dirname(self.strPath), _strPathToPyarchDirectory=strPyarchPath)
xsDataResultSimpleHTMLPage.setPathToHTMLDirectory(XSDataFile(XSDataString(strPyarchPath)))
if not os.path.exists(strPyarchPath):
os.makedirs(strPyarchPath, 0o755)
shutil.copy(pathToJsonFile, strPyarchPath)
pathToJsonFile = os.path.join(strPyarchPath, os.path.basename(pathToJsonFile))
# Write json file
xsDataResultSimpleHTMLPage.pathToJsonFile = XSDataFile(XSDataString(pathToJsonFile))
self.setDataOutput(xsDataResultSimpleHTMLPage)
def eiger_template_to_image(self, fmt, num):
fileNumber = int(num / 100)
if fileNumber == 0:
fileNumber = 1
if EDUtilsPath.isMAXIV():
fmt_string = fmt.replace("%06d", "data_%06d" % fileNumber)
else:
fmt_string = fmt.replace("####", "1_data_%06d" % fileNumber)
return fmt_string.format(num)
def __init__(self):
EDLogging.__init__(self)
Thread.__init__(self)
self.__edSlotPreProcess = EDSlot()
self.__edSlotProcess = EDSlot()
self.__edSlotPostProcess = EDSlot()
self.__edSlotSUCCESS = EDSlot()
self.__edSlotFAILURE = EDSlot()
self.__edSlotFinallyProcess = EDSlot()
self.__bIsFailure = False
self.__bIsTimeOut = False
self.__fTimeOutInSeconds = None
if EDUtilsPath.isEMBL() or EDUtilsPath.isALBA() or EDUtilsPath.isMAXIV(
):
self.__fDefaultTimeOutInSeconds = 3600.0
else:
self.__fDefaultTimeOutInSeconds = 600.0
self.__bIsAbort = False
# Reference to the object which calls execute or executeSynchronous
self.__edObject = None
self.__lExtraTime = [
] # list of extra allowed time for execution (in second)
self.__bLogTiming = False
def eiger_template_to_master(self, fmt):
if EDUtilsPath.isMAXIV():
fmt_string = fmt.replace("%06d", "master")
else:
fmt_string = fmt.replace("####", "1_master")
return fmt_string
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG('EDPluginControlAutoPROCv1_0.process starting')
directory = None
template = None
imageNoStart = None
imageNoEnd = None
pathToStartImage = None
pathToEndImage = None
userName = os.environ["USER"]
beamline = "unknown"
proposal = "unknown"
# If we have a data collection id, use it
if self.dataInput.dataCollectionId is not None:
# Recover the data collection from ISPyB
xsDataInputRetrieveDataCollection = XSDataInputRetrieveDataCollection()
identifier = str(self.dataInput.dataCollectionId.value)
xsDataInputRetrieveDataCollection.dataCollectionId = self.dataInput.dataCollectionId
self.edPluginRetrieveDataCollection.dataInput = xsDataInputRetrieveDataCollection
self.edPluginRetrieveDataCollection.executeSynchronous()
ispybDataCollection = self.edPluginRetrieveDataCollection.dataOutput.dataCollection
directory = ispybDataCollection.imageDirectory
if EDUtilsPath.isEMBL():
template = ispybDataCollection.fileTemplate.replace("%05d", "#" * 5)
elif EDUtilsPath.isMAXIV():
template = ispybDataCollection.fileTemplate
else:
template = ispybDataCollection.fileTemplate.replace("%04d", "####")
if self.dataInput.fromN is None:
imageNoStart = ispybDataCollection.startImageNumber
else:
imageNoStart = self.dataInput.fromN.value
if self.dataInput.toN is None:
imageNoEnd = imageNoStart + ispybDataCollection.numberOfImages - 1
else:
imageNoEnd = self.dataInput.toN.value
# # DEBUG we set the end image to 20 in order to speed up things
# self.warning("End image set to 20 (was {0})".format(imageNoEnd))
# imageNoEnd = 20
pathToStartImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, ispybDataCollection.fileTemplate % imageNoEnd)
else:
identifier = str(int(time.time()))
directory = self.dataInput.dirN.path.value
template = self.dataInput.templateN.value
imageNoStart = self.dataInput.fromN.value
imageNoEnd = self.dataInput.toN.value
if EDUtilsPath.isEMBL():
fileTemplate = template.replace("#####", "%05d")
else:
fileTemplate = template.replace("####", "%04d")
pathToStartImage = os.path.join(directory, fileTemplate % imageNoStart)
pathToEndImage = os.path.join(directory, fileTemplate % imageNoEnd)
# Try to get proposal from path
if EDUtilsPath.isESRF():
listDirectory = directory.split(os.sep)
try:
if listDirectory[1] == "data":
if listDirectory[2] == "visitor":
beamline = listDirectory[4]
proposal = listDirectory[3]
else:
beamline = listDirectory[2]
proposal = listDirectory[4]
except:
beamline = "unknown"
proposal = userName
if imageNoEnd - imageNoStart < 8:
error_message = "There are fewer than 8 images, aborting"
self.addErrorMessage(error_message)
self.ERROR(error_message)
self.setFailure()
return
# Process directory
if self.dataInput.processDirectory is not None:
processDirectory = self.dataInput.processDirectory.path.value
else:
processDirectory = directory.replace("RAW_DATA", "PROCESSED_DATA")
# Make results directory
if EDUtilsPath.isALBA():
_processDirectory = "_".join(pathToStartImage.split('_')[:-1])
from datetime import datetime
_id = datetime.now().strftime('%Y%m%d_%H%M%S')
self.resultsDirectory = os.path.join(_processDirectory, "autoPROC_%s" % _id)
else:
self.resultsDirectory = os.path.join(processDirectory, "results")
if not os.path.exists(self.resultsDirectory):
os.makedirs(self.resultsDirectory, 0o755)
# Create path to pyarch
if self.dataInput.reprocess is not None and self.dataInput.reprocess.value:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchReprocessDirectoryPath(beamline,
"autoPROC", self.dataInput.dataCollectionId.value)
else:
self.pyarchDirectory = EDHandlerESRFPyarchv1_0.createPyarchFilePath(self.resultsDirectory)
if self.pyarchDirectory is not None:
self.pyarchDirectory = self.pyarchDirectory.replace('PROCESSED_DATA', 'RAW_DATA')
if not os.path.exists(self.pyarchDirectory):
try:
os.makedirs(self.pyarchDirectory, 0o755)
except:
self.pyarchDirectory = None
# The resultsDirectory is not used at ALBA (only pyarchDirectory)
if EDUtilsPath.isALBA():
self.resultsDirectory = None
# Determine pyarch prefix
if EDUtilsPath.isALBA():
listPrefix = template.split("_")
self.pyarchPrefix = "ap_{0}_{1}".format("_".join(listPrefix[:-2]),
listPrefix[-2])
else:
listPrefix = template.split("_")
self.pyarchPrefix = "ap_{0}_run{1}".format(listPrefix[-3], listPrefix[-2])
isH5 = False
if any(beamline in pathToStartImage for beamline in ["id30b"]):
minSizeFirst = 6000000
minSizeLast = 6000000
elif any(beamline in pathToStartImage for beamline in ["id23eh2", "id30a1"]):
minSizeFirst = 2000000
minSizeLast = 2000000
elif any(beamline in pathToStartImage for beamline in ["id23eh1", "id30a3"]):
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
else:
minSizeFirst = 1000000
minSizeLast = 1000000
if EDUtilsPath.isMAXIV():
minSizeFirst = 100000
minSizeLast = 100000
pathToStartImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoStart))
pathToEndImage = os.path.join(directory,
self.eiger_template_to_image(template, imageNoEnd))
isH5 = True
if EDUtilsPath.isEMBL() or EDUtilsPath.isMAXIV():
fWaitFileTimeout = 60 # s
else:
fWaitFileTimeout = 3600 # s
xsDataInputMXWaitFileFirst = XSDataInputMXWaitFile()
xsDataInputMXWaitFileFirst.file = XSDataFile(XSDataString(pathToStartImage))
xsDataInputMXWaitFileFirst.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileFirst.size = XSDataInteger(minSizeFirst)
self.edPluginWaitFileFirst.dataInput = xsDataInputMXWaitFileFirst
self.edPluginWaitFileFirst.executeSynchronous()
if self.edPluginWaitFileFirst.dataOutput.timedOut.value:
strWarningMessage = "Timeout after %d seconds waiting for the first image %s!" % (fWaitFileTimeout, pathToStartImage)
self.addWarningMessage(strWarningMessage)
self.WARNING(strWarningMessage)
xsDataInputMXWaitFileLast = XSDataInputMXWaitFile()
xsDataInputMXWaitFileLast.file = XSDataFile(XSDataString(pathToEndImage))
xsDataInputMXWaitFileLast.timeOut = XSDataTime(fWaitFileTimeout)
self.edPluginWaitFileLast.size = XSDataInteger(minSizeLast)
self.edPluginWaitFileLast.dataInput = xsDataInputMXWaitFileLast
self.edPluginWaitFileLast.executeSynchronous()
if self.edPluginWaitFileLast.dataOutput.timedOut.value:
strErrorMessage = "Timeout after %d seconds waiting for the last image %s!" % (fWaitFileTimeout, pathToEndImage)
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
self.timeStart = time.localtime()
if self.dataInput.dataCollectionId is not None:
# Set ISPyB to running
if self.doAnom:
self.autoProcIntegrationIdAnom, self.autoProcProgramIdAnom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingProgram,
isAnom=True,
timeStart=self.timeStart)
self.autoProcIntegrationIdAnomStaraniso, self.autoProcProgramIdAnomStaraniso = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingProgramStaraniso,
isAnom=True,
timeStart=self.timeStart)
if self.doNoanom:
self.autoProcIntegrationIdNoanom, self.autoProcProgramIdNoanom = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingProgram,
isAnom=False,
timeStart=self.timeStart)
self.autoProcIntegrationIdNoanomStaraniso, self.autoProcProgramIdNoanomStaraniso = \
EDHandlerXSDataISPyBv1_4.setIspybToRunning(self, dataCollectionId=self.dataInput.dataCollectionId.value,
processingCommandLine=self.processingCommandLine,
processingPrograms=self.processingProgramStaraniso,
isAnom=False,
timeStart=self.timeStart)
# Prepare input to execution plugin
if self.doAnom:
xsDataInputAutoPROCAnom = XSDataInputAutoPROC()
xsDataInputAutoPROCAnom.anomalous = XSDataBoolean(True)
xsDataInputAutoPROCAnom.symm = self.dataInput.symm
xsDataInputAutoPROCAnom.cell = self.dataInput.cell
xsDataInputAutoPROCAnom.lowResolutionLimit = self.dataInput.lowResolutionLimit
xsDataInputAutoPROCAnom.highResolutionLimit = self.dataInput.highResolutionLimit
if self.doNoanom:
xsDataInputAutoPROCNoanom = XSDataInputAutoPROC()
xsDataInputAutoPROCNoanom.anomalous = XSDataBoolean(False)
xsDataInputAutoPROCNoanom.symm = self.dataInput.symm
xsDataInputAutoPROCNoanom.cell = self.dataInput.cell
xsDataInputAutoPROCNoanom.lowResolutionLimit = self.dataInput.lowResolutionLimit
xsDataInputAutoPROCNoanom.highResolutionLimit = self.dataInput.highResolutionLimit
xsDataAutoPROCIdentifier = XSDataAutoPROCIdentifier()
xsDataAutoPROCIdentifier.idN = XSDataString(identifier)
xsDataAutoPROCIdentifier.dirN = XSDataFile(XSDataString(directory))
xsDataAutoPROCIdentifier.templateN = XSDataString(template)
xsDataAutoPROCIdentifier.fromN = XSDataInteger(imageNoStart)
xsDataAutoPROCIdentifier.toN = XSDataInteger(imageNoEnd)
if self.doAnom:
xsDataInputAutoPROCAnom.addIdentifier(xsDataAutoPROCIdentifier)
if self.doNoanom:
xsDataInputAutoPROCNoanom.addIdentifier(xsDataAutoPROCIdentifier.copy())
if isH5:
masterFilePath = os.path.join(directory,
self.eiger_template_to_master(template))
if self.doAnom:
xsDataInputAutoPROCAnom.masterH5 = XSDataFile(XSDataString(masterFilePath))
if self.doNoanom:
xsDataInputAutoPROCNoanom.masterH5 = XSDataFile(XSDataString(masterFilePath))
timeStart = time.localtime()
if self.doAnom:
self.edPluginExecAutoPROCAnom.dataInput = xsDataInputAutoPROCAnom
self.edPluginExecAutoPROCAnom.execute()
if self.doNoanom:
self.edPluginExecAutoPROCNoanom.dataInput = xsDataInputAutoPROCNoanom
self.edPluginExecAutoPROCNoanom.execute()
if self.doAnom:
self.edPluginExecAutoPROCAnom.synchronize()
if self.doNoanom:
self.edPluginExecAutoPROCNoanom.synchronize()
timeEnd = time.localtime()
# Upload to ISPyB
if self.doAnom:
self.uploadToISPyB(self.edPluginExecAutoPROCAnom, True, False, proposal, timeStart, timeEnd)
self.uploadToISPyB(self.edPluginExecAutoPROCAnom, True, True, proposal, timeStart, timeEnd)
if self.doNoanom:
self.uploadToISPyB(self.edPluginExecAutoPROCNoanom, False, False, proposal, timeStart, timeEnd)
self.uploadToISPyB(self.edPluginExecAutoPROCNoanom, False, True, proposal, timeStart, timeEnd)
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlPyarchThumbnailGeneratorv1_0.preProcess")
# Check that the input image exists and is of the expected type
strPathToDiffractionImage = self.dataInput.diffractionImage.path.value
strImageFileNameExtension = os.path.splitext(
strPathToDiffractionImage)[1]
if not strImageFileNameExtension in [
".img", ".marccd", ".mccd", ".cbf", ".h5"
]:
self.error(
"Unknown image file name extension for pyarch thumbnail generator: %s"
% strPathToDiffractionImage)
self.setFailure()
else:
# Load the MXWaitFile plugin
xsDataInputMXWaitFile = XSDataInputMXWaitFile()
pathToImageFile = strPathToDiffractionImage
# Quite ugly hack to avoid lag problems at the ESRF:
if EDUtilsPath.isESRF() or EDUtilsPath.isALBA(
) or EDUtilsPath.isMAXIV():
if any(beamline in strPathToDiffractionImage
for beamline in ["id30b"]):
# Pilatus 6M
self.minImageSize = 6000000
elif any(beamline in strPathToDiffractionImage
for beamline in ["id23eh2", "id30a1"]):
# Pilatus3 2M
self.minImageSize = 2000000
elif strImageFileNameExtension == ".h5":
self.h5MasterFilePath, self.h5DataFilePath, self.h5FileNumber = self.getH5FilePath(
pathToImageFile)
pathToImageFile = self.h5DataFilePath
self.isH5 = True
elif EDUtilsPath.isEMBL():
self.minImageSize = 10000
xsDataInputMXWaitFile.setSize(XSDataInteger(self.minImageSize))
xsDataInputMXWaitFile.setFile(
XSDataFile(XSDataString(pathToImageFile)))
if self.getDataInput().getWaitForFileTimeOut():
xsDataInputMXWaitFile.setTimeOut(
self.getDataInput().getWaitForFileTimeOut())
self.edPluginMXWaitFile = self.loadPlugin(
self.strMXWaitFilePluginName)
self.edPluginMXWaitFile.setDataInput(xsDataInputMXWaitFile)
# Load the execution plugin
self.edPluginExecThumbnail = self.loadPlugin(
self.strExecThumbnailPluginName)
xsDataInputMXThumbnail = XSDataInputMXThumbnail()
xsDataInputMXThumbnail.image = self.getDataInput(
).getDiffractionImage()
xsDataInputMXThumbnail.height = XSDataInteger(1024)
xsDataInputMXThumbnail.width = XSDataInteger(1024)
xsDataInputMXThumbnail.format = self.dataInput.format
# Output path
strImageNameWithoutExt = os.path.basename(
os.path.splitext(strPathToDiffractionImage)[0])
strImageDirname = os.path.dirname(strPathToDiffractionImage)
if self.getDataInput().getForcedOutputDirectory():
strForcedOutputDirectory = self.getDataInput(
).getForcedOutputDirectory().getPath().getValue()
if not os.access(strForcedOutputDirectory, os.W_OK):
self.error("Cannot write to forced output directory : %s" %
strForcedOutputDirectory)
self.setFailure()
else:
self.strOutputPathWithoutExtension = os.path.join(
strForcedOutputDirectory, strImageNameWithoutExt)
else:
# Try to store in the ESRF pyarch directory
strOutputDirname = EDHandlerESRFPyarchv1_0.createPyarchFilePath(
strImageDirname)
# Check that output pyarch path exists and is writeable:
bIsOk = False
if strOutputDirname:
if not os.path.exists(strOutputDirname):
# Try to create the directory
try:
os.makedirs(strOutputDirname)
bIsOk = True
except Exception as e:
self.WARNING("Couldn't create the directory %s" %
strOutputDirname)
elif os.access(strOutputDirname, os.W_OK):
bIsOk = True
if not bIsOk:
self.warning("Cannot write to pyarch directory: %s" %
strOutputDirname)
strTmpUser = os.path.join("/tmp", os.environ["USER"])
if not os.path.exists(strTmpUser):
os.mkdir(strTmpUser, 0o755)
strOutputDirname = tempfile.mkdtemp(
prefix="EDPluginPyarchThumbnailv10_", dir=strTmpUser)
os.chmod(strOutputDirname, 0o755)
self.warning("Writing thumbnail images to: %s" %
strOutputDirname)
self.strOutputPathWithoutExtension = os.path.join(
strOutputDirname, strImageNameWithoutExt)
if self.dataInput.format is not None:
self.strSuffix = self.dataInput.format.value.lower()
self.strImageFormat = self.dataInput.format.value.upper()
self.strOutputPath = os.path.join(
self.strOutputPathWithoutExtension + "." + self.strSuffix)
xsDataInputMXThumbnail.setOutputPath(
XSDataFile(XSDataString(self.strOutputPath)))
self.edPluginExecThumbnail.setDataInput(xsDataInputMXThumbnail)
def createPyarchFilePath(_strESRFPath):
"""
This method translates from an ESRF "visitor" path to a "pyarch" path:
/data/visitor/mx415/id14eh1/20100209 -> /data/pyarch/2010/id14eh1/mx415/20100209
"""
strPyarchDNAFilePath = None
listOfDirectories = _strESRFPath.split(os.sep)
if EDUtilsPath.isALBA():
return EDHandlerESRFPyarchv1_0.translateToIspybALBAPath(
_strESRFPath)
if EDUtilsPath.isEMBL():
if 'p13' in listOfDirectories[0:3] or 'P13' in listOfDirectories[
0:3]:
strPyarchDNAFilePath = os.path.join('/data/ispyb/p13',
*listOfDirectories[4:])
else:
strPyarchDNAFilePath = os.path.join('/data/ispyb/p14',
*listOfDirectories[4:])
return strPyarchDNAFilePath
if EDUtilsPath.isMAXIV():
strPyarchDNAFilePath = _strESRFPath.replace(
"/data", "/mxn/groups/ispybstorage", 1)
return strPyarchDNAFilePath
listBeamlines = [
"bm07", "id14eh1", "id14eh2", "id14eh3", "id14eh4", "id23eh1",
"id23eh2", "id29", "id30a1", "id30a2", "id30a3", "id30b",
"simulator_mxcube"
]
# Check that we have at least four levels of directories:
if (len(listOfDirectories) > 5):
strDataDirectory = listOfDirectories[1]
strSecondDirectory = listOfDirectories[2]
strThirdDirectory = listOfDirectories[3]
strFourthDirectory = listOfDirectories[4]
strFifthDirectory = listOfDirectories[5]
year = strFifthDirectory[0:4]
strProposal = None
strBeamline = None
if (strDataDirectory == "data") and (strSecondDirectory == "gz"):
if strThirdDirectory == "visitor":
strProposal = strFourthDirectory
strBeamline = strFifthDirectory
elif strFourthDirectory == "inhouse":
strProposal = strFifthDirectory
strBeamline = strThirdDirectory
else:
raise RuntimeError(
"Illegal path for EDHandlerESRFPyarchv1_0.createPyarchFilePath: {0}"
.format(_strESRFPath))
listOfRemainingDirectories = listOfDirectories[6:]
elif (strDataDirectory == "data") and (strSecondDirectory
== "visitor"):
strProposal = listOfDirectories[3]
strBeamline = listOfDirectories[4]
listOfRemainingDirectories = listOfDirectories[5:]
elif ((strDataDirectory == "data")
and (strSecondDirectory in listBeamlines)):
strBeamline = strSecondDirectory
strProposal = listOfDirectories[4]
listOfRemainingDirectories = listOfDirectories[5:]
if (strProposal != None) and (strBeamline != None):
strPyarchDNAFilePath = os.path.join(os.sep, "data")
strPyarchDNAFilePath = os.path.join(strPyarchDNAFilePath,
"pyarch")
strPyarchDNAFilePath = os.path.join(strPyarchDNAFilePath, year)
strPyarchDNAFilePath = os.path.join(strPyarchDNAFilePath,
strBeamline)
strPyarchDNAFilePath = os.path.join(strPyarchDNAFilePath,
strProposal)
for strDirectory in listOfRemainingDirectories:
strPyarchDNAFilePath = os.path.join(
strPyarchDNAFilePath, strDirectory)
if (strPyarchDNAFilePath is None):
EDVerbose.WARNING(
"EDHandlerESRFPyarchv1_0.createPyArchFilePath: path not converted for pyarch: %s "
% _strESRFPath)
return strPyarchDNAFilePath
