def parse(self):
"""
parse options from command line
"""
parser = optparse.OptionParser()
parser.add_option("-V", "--version", dest="version", action="store_true",
help="print version of the program and quit", metavar="FILE", default=False)
parser.add_option("-v", "--verbose",
action="store_true", dest="debug", default=False,
help="switch to debug/verbose mode")
parser.add_option("-m", "--mask", dest="mask",
help="file containing the mask (for image reconstruction)", default=None)
parser.add_option("-M", "--mode", dest="mode",
help="Mode can be online/offline/all", default="offline")
parser.add_option("-o", "--out", dest="output",
help="file for log", default=None)
parser.add_option("-w", "--wavelength", dest="wavelength", type="float",
help="wavelength of the X-Ray beam in Angstrom", default=None)
parser.add_option("-e", "--energy", dest="energy", type="float",
help="energy of the X-Ray beam in keV (hc=%skeV.A)" % self.hc, default=None)
parser.add_option("-t", "--template", dest="template", type="str",
help="template XML file", default=None)
parser.add_option("-n", "--nbcpu", dest="nbcpu", type="int",
help="template XML file", default=self.nbcpu)
(options, args) = parser.parse_args()
# Analyse aruments and options
if options.version:
print("BioSaxs Azimuthal integration version %s" % __version__)
sys.exit(0)
if options.debug:
EDVerbose.setVerboseDebugOn()
self.debug = True
if options.output:
EDVerbose.setLogFileName(options.output)
if options.mask and os.path.isfile(options.mask):
self.maskfile = options.mask
if options.template and os.path.isfile(options.template):
self.xml = open(options.template).read()
if options.wavelength:
self.wavelength = 1e-10 * options.wavelength
elif options.energy:
self.wavelength = 1e-10 * self.hc / options.energy
if options.mode=="offline":
self.mode = "offline"
self.newerOnly = False
elif options.mode=="online":
self.mode = "dirwarch"
self.newerOnly = True
elif options.mode=="dirwatch":
self.mode = "dirwarch"
self.newerOnly = False
self.cpu_sem = Semaphore(options.nbcpu)
self.nbcpu = options.nbcpu
self.dataFiles = [f for f in args if os.path.isfile(f)]
if not self.dataFiles:
raise RuntimeError("Please provide datafiles or read the --help")
def runMXv1Pipeline():
strLogFileName = os.path.join(returnWorkingDirectory(), "wsgi-server.log")
EDVerbose.setLogFileName(strLogFileName)
strInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if strInput:
# Take the parameters string, split off the title and run the bash script to generate the input char. XML
listParams = shlex.split(strInput)
strComments = listParams[0] # the 1st item
strShortComments = listParams[1] # the 2nd item
strWorkingDir = listParams[2] # the 3rd item
strHTMLResultDir = listParams[3] # the 4th item
os.chdir(strWorkingDir)
strParamString = " ".join(listParams[4:]) # all but the first four items
edPluginMxv1ParamsToXML = EDFactoryPluginStatic.loadPlugin('EDPluginMxv1ParamsToXMLv1_0')
edPluginMxv1ParamsToXML.setDataInput(XSDataString(strParamString), "paramString")
edPluginMxv1ParamsToXML.executeSynchronous()
xsDataFile = edPluginMxv1ParamsToXML.getDataOutput()
# Read the XML and parse it into an object hierarchy
strXMLFile = xsDataFile.getPath().getValue()
f = open(strXMLFile, 'r')
xml = f.read()
f.close()
xsDataInputCharacterisation = XSDataInputCharacterisation.parseString(xml)
# Run the MXv1 application pipeline
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath, \
_xsDataInputCharacterisation=xsDataInputCharacterisation, \
_strComments=strComments, \
_strShortComments=strShortComments)
edApplicationMXv1Characterisation.execute()
# Run the EDNA2HTML generator on the output from the MXv1 application
edPluginExecOutputHTML = EDFactoryPluginStatic.loadPlugin('EDPluginExecOutputHTMLv1_0')
edPluginExecOutputHTML.setDataInput(XSDataString(strComments), "title")
strWorkingDir = os.path.join(strWorkingDir, edApplicationMXv1Characterisation.getWorkingDir())
edPluginExecOutputHTML.setDataInput(XSDataString(strWorkingDir), "workingDir")
#strBaseDir = os.path.join(strHTMLResultDir, "edna")
#edPluginExecOutputHTML.setDataInput(XSDataString(strBaseDir), "basename")
edPluginExecOutputHTML.setDataInput(XSDataString(strHTMLResultDir), "basename")
edPluginExecOutputHTML.executeSynchronous()
strPathToHTMLFile = ""
if (edPluginExecOutputHTML.hasDataOutput("htmlFile")):
strPathToHTMLFile = edPluginExecOutputHTML.getDataOutput("htmlFile")[0].getPath().getValue()
else:
EDVerbose.ERROR("edna-mxv1-wsgi-server: edPluginExecOutputHTML has no dataOutput htmlFile!")
if strPathToHTMLFile =="":
EDVerbose.ERROR("edna-mxv1-wsgi-server: Returning empty string")
return strPathToHTMLFile
else:
return strInput
def processCommandline(self):
"""
This method is intended to be overridden by applications who
would like to implement their own command line handling.
This default method implements the following workflow:
- Check for debug, verbose and log file command line options
"""
EDVerbose.DEBUG("EDApplication.execute")
EDVerbose.log(self.__edCommandLine.getCommandLine())
self.processCommandLineDebugVerboseLogFile()
# Determine the base directory
if (self.__strBaseDir is None):
self.processCommandLineBaseDirectory()
# Set the name of the log file
self.__strPathToLogFile = os.path.abspath(
os.path.join(self.__strBaseDir, self.__strLogFileName))
EDVerbose.setLogFileName(self.__strPathToLogFile)
self.processCommandLineHelp()
if (not self.__bIsFailure):
self.processCommandLineVersion()
if (not self.__bIsFailure):
# Name of the plugin to be executed
if (self.__strPluginName is None):
self.processCommandLinePluginName()
# Path to the input XML file
if (self.__strDataInputFilePath is None):
self.processCommandLineInputFilePath()
# Path to the output XML file
if (self.__strDataOutputFilePath is None):
self.processCommandLineOutputFilePath()
if (self.__bIsFailure):
self.usage()
if (not self.__bIsFailure):
# If strConfigurationFileName is None, this means that it has not been given to the constructor\
# It has been given by the command line\
if (self.__strConfigurationFileName is None):
self.__strConfigurationFileName = self.getCommandLineArgument(
EDApplication.CONFIGURATION_PARAM_LABEL)
def processCommandline(self):
"""
This method is intended to be overridden by applications who
would like to implement their own command line handling.
This default method implements the following workflow:
- Check for debug, verbose and log file command line options
"""
EDVerbose.DEBUG("EDApplication.execute")
EDVerbose.log(self.__edCommandLine.getCommandLine())
self.processCommandLineDebugVerboseLogFile()
# Determine the base directory
if(self.__strBaseDir is None):
self.processCommandLineBaseDirectory()
# Set the name of the log file
self.__strPathToLogFile = os.path.abspath(os.path.join(self.__strBaseDir, self.__strLogFileName))
EDVerbose.setLogFileName(self.__strPathToLogFile)
self.processCommandLineHelp()
if (not self.__bIsFailure):
self.processCommandLineVersion()
if (not self.__bIsFailure):
# Name of the plugin to be executed
if (self.__strPluginName is None):
self.processCommandLinePluginName()
# Path to the input XML file
if (self.__strDataInputFilePath is None):
self.processCommandLineInputFilePath()
# Path to the output XML file
if(self.__strDataOutputFilePath is None):
self.processCommandLineOutputFilePath()
if (self.__bIsFailure):
self.usage()
if (not self.__bIsFailure):
# If strConfigurationFileName is None, this means that it has not been given to the constructor\
# It has been given by the command line\
if(self.__strConfigurationFileName is None):
self.__strConfigurationFileName = self.getCommandLineArgument(EDApplication.CONFIGURATION_PARAM_LABEL)
def preProcess(self):
"""
Scans the command line.
"""
EDVerbose.DEBUG("EDTestLauncher.preProcess")
edCommandLine = EDCommandLine(sys.argv)
EDVerbose.log(self.getEdCommandLine().getCommandLine())
self.processCommandLineDebugVerboseLogFile()
bContinue = True
strTestName = edCommandLine.getArgument(EDTestLauncher.TEST_LABEL)
EDVerbose.DEBUG("EDTestLauncher.preProcess: test name = %r" % strTestName)
if (strTestName is None):
EDVerbose.screen("ERROR - no --test argument found")
bContinue = False
else:
self.__edTestCase = EDUtilsTest.getFactoryPluginTest().loadPlugin(strTestName)
if (bContinue):
# Determine the base directory
if(self.getBaseDir() is None):
self.processCommandLineBaseDirectory()
# Create the application working directory
strApplicationInstanceName = strTestName + "_" + time.strftime("%Y%m%d-%H%M%S", time.localtime())
if(self.getWorkingDir() is None):
self.setWorkingDir(strApplicationInstanceName)
self.createApplicationWorkingDirectory()
# Set the name of the log file
EDVerbose.setLogFileName(os.path.join(self.getBaseDir(), strApplicationInstanceName + ".log"))
# The check for --quiet and --DEBUG should ideally be placed elsewhere,
# for example in EDApplication.
if (edCommandLine.existCommand(EDTestLauncher.QUIET_LABEL)):
EDVerbose.setVerboseOff()
EDVerbose.setTestOff()
if (edCommandLine.existCommand(EDApplication.DEBUG_PARAM_LABEL_1) or \
edCommandLine.existCommand(EDApplication.DEBUG_PARAM_LABEL_2)):
EDVerbose.setVerboseDebugOn()
EDVerbose.DEBUG("EDTestLauncher.preProcess: Debug mode")
if __name__ == '__main__':
EDVerbose.setVerboseDebugOn()
# Sleep a random time 0-2s in order to avoid problems if many instances started at the same time
fSleepTime = random.random()*2.0
EDVerbose.DEBUG("Sleeping for %.2f s" % fSleepTime)
time.sleep(fSleepTime)
# Popolate input data
EDVerbose.screen("Starting id29_create_thumbnail")
# If no arguments stop
if len(sys.argv) <= 2:
EDVerbose.screen("Usage: id29_create_thumbnail image_directory_path image1 [image2]" )
sys.exit(1)
EDVerbose.screen("Arguments: %r" % sys.argv)
strPathToTempDir = tempfile.mkdtemp(prefix="id29_create_thumbnail_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "id29_create_thumbnail.log"))
strImageDirectory = sys.argv[1]
listImageName = sys.argv[2:]
# Quick check if the two image names are the same. If they are launch the thumbnail generator only once
if len(listImageName) == 2:
if listImageName[0] == listImageName[1]:
listImageName = [ listImageName[0] ]
for strImageName in listImageName:
xsDataInputPyarchThumbnailGenerator = XSDataInputPyarchThumbnailGenerator()
xsDataInputPyarchThumbnailGenerator.setWaitForFileTimeOut(XSDataTime(1000))
strImagePath = os.path.join(strImageDirectory, strImageName)
xsDataInputPyarchThumbnailGenerator.setDiffractionImage(XSDataFile(XSDataString(strImagePath)))
EDVerbose.screen("XML input for EDPluginControlPyarchThumbnailGeneratorv1_0: %s" % xsDataInputPyarchThumbnailGenerator.marshal())
edPluginControlPyarchThumbnailGeneratorv1_0 = EDPluginControlPyarchThumbnailGeneratorv1_0()
edPluginControlPyarchThumbnailGeneratorv1_0.setDataInput(xsDataInputPyarchThumbnailGenerator)
edPluginControlPyarchThumbnailGeneratorv1_0.execute()
from EDVerbose import EDVerbose
from EDFactoryPluginStatic import EDFactoryPluginStatic
from XSDataCommon import XSDataFile
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
from XSDataCommon import XSDataBoolean
EDFactoryPluginStatic.loadModule("XSDataGridScreeningv1_0")
from XSDataGridScreeningv1_0 import XSDataInputGridScreening
if __name__ == '__main__':
strPathToTempDir = tempfile.mkdtemp(
prefix="edna-image-quality-indicators_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "edna.log"))
# Popolate input data
EDVerbose.screen("Starting EDNA image quality indicators processing")
EDVerbose.screen("Arguments: %r" % sys.argv)
bVerbose = False
bDebug = False
listPaths = []
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
if os.path.exists(strArg):
listPaths.append(os.path.abspath(strArg))
for strPath in listPaths:
from XSDataISPyBv1_4 import XSDataInputStoreAutoProc
from XSDataISPyBv1_4 import AutoProcContainer
def successAction(self, _edObject=None):
EDVerbose.screen("XML data sucessfully stored in ISPyB")
def failureAction(self, _edObject=None):
EDVerbose.ERROR("XML data not stored in ISPyB")
if __name__ == '__main__':
strCwd = os.getcwd()
strPathToTempDir = tempfile.mkdtemp(prefix="edna-autoproc2ispyb_")
os.chdir(strPathToTempDir)
EDVerbose.setVerboseOn()
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "edna.log"))
# Populate input data
EDVerbose.DEBUG("Arguments: %r" % sys.argv)
bVerbose = False
bDebug = False
listPaths = []
for iIndex, strArg in enumerate(sys.argv[1:]):
strarg = strArg.lower()
if strarg == "--verbose":
EDVerbose.setVerboseOn()
elif strarg == "--debug":
EDVerbose.setVerboseDebugOn()
strArgPath = strArg
if os.path.dirname(strArgPath) == "":
strArgPath = os.path.join(strCwd, strArg)
strArgPathAbsolute = os.path.abspath(strArgPath)
# Sleep a random time 0-2s in order to avoid problems if many instances started at the same time
fSleepTime = random.random() * 2.0
EDVerbose.DEBUG("Sleeping for %.2f s" % fSleepTime)
time.sleep(fSleepTime)
# Popolate input data
EDVerbose.screen("Starting id29_create_thumbnail")
# If no arguments stop
if len(sys.argv) <= 2:
EDVerbose.screen(
"Usage: id29_create_thumbnail image_directory_path image1 [image2]"
)
sys.exit(1)
EDVerbose.screen("Arguments: %r" % sys.argv)
strPathToTempDir = tempfile.mkdtemp(prefix="id29_create_thumbnail_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(
os.path.join(strPathToTempDir, "id29_create_thumbnail.log"))
strImageDirectory = sys.argv[1]
listImageName = sys.argv[2:]
# Quick check if the two image names are the same. If they are launch the thumbnail generator only once
if len(listImageName) == 2:
if listImageName[0] == listImageName[1]:
listImageName = [listImageName[0]]
for strImageName in listImageName:
xsDataInputPyarchThumbnailGenerator = XSDataInputPyarchThumbnailGenerator(
)
xsDataInputPyarchThumbnailGenerator.setWaitForFileTimeOut(
XSDataTime(1000))
strImagePath = os.path.join(strImageDirectory, strImageName)
xsDataInputPyarchThumbnailGenerator.setDiffractionImage(
XSDataFile(XSDataString(strImagePath)))
EDVerbose.screen(
def runEdnaPlugin(execPath, pluginName, isDebug, xml, additionalPaths=None):
'''
execPath - path to run plugin in
pluginName - plugin name
isDebug - True if should run edna in debug mode
xml - xml input to edna
additionalPaths - list of other python path locations
You must set EDNA_HOME to use this method
This method blocks until the EDJob has reached a final status
'''
if (not 'EDNA_HOME' in os.environ):
raise Exception("Cannot locate EDNA_HOME. Please set before running Edna plugins.")
if (not 'EDNA_SITE' in os.environ):
raise Exception(" Please set EDNA_SITE before running Edna plugins.")
'''
Add edna to path
'''
ednaKernelPath = os.environ['EDNA_HOME']+"/kernel/src"
sys.path.insert(0, ednaKernelPath)
'''
If there are any additional paths such as fabio, add these
'''
if (not additionalPaths is None and len(additionalPaths)>0):
for path in additionalPaths:
sys.path.append(path)
os.chdir(execPath)
from EDVerbose import EDVerbose
if (isDebug):
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseOn()
EDVerbose.setVerboseDebugOff()
from EDJob import EDJob
EDVerbose.setLogFileName(execPath+"/"+pluginName+".log")
edJob = EDJob(pluginName)
edJob.setDataInput(xml)
edJob.execute()
edJob.synchronize() # In theory should mean that the following loop is not needed
# Unhelpful way of waiting for EDJob to be finished
# TODO Fix this in EDJob some time
while(True):
status = edJob.getStatus()
if (status is None):
time.sleep(0.2) # 200 ms
continue
if ("failure" == status):
raise Exception("EDJob failed! ")
if ("success" == status):
break
ret = edJob.getDataOutput()
return str(ret)
def runEdnaPlugin(execPath, pluginName, isDebug, xml, additionalPaths=None):
'''
execPath - path to run plugin in
pluginName - plugin name
isDebug - True if should run edna in debug mode
xml - xml input to edna
additionalPaths - list of other python path locations
You must set EDNA_HOME to use this method
This method blocks until the EDJob has reached a final status
'''
if (not 'EDNA_HOME' in os.environ):
raise Exception(
"Cannot locate EDNA_HOME. Please set before running Edna plugins.")
if (not 'EDNA_SITE' in os.environ):
raise Exception(" Please set EDNA_SITE before running Edna plugins.")
'''
Add edna to path
'''
ednaKernelPath = os.environ['EDNA_HOME'] + "/kernel/src"
sys.path.insert(0, ednaKernelPath)
'''
If there are any additional paths such as fabio, add these
'''
if (not additionalPaths is None and len(additionalPaths) > 0):
for path in additionalPaths:
sys.path.append(path)
os.chdir(execPath)
from EDVerbose import EDVerbose
if (isDebug):
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseOn()
EDVerbose.setVerboseDebugOff()
from EDJob import EDJob
EDVerbose.setLogFileName(execPath + "/" + pluginName + ".log")
edJob = EDJob(pluginName)
edJob.setDataInput(xml)
edJob.execute()
edJob.synchronize(
) # In theory should mean that the following loop is not needed
# Unhelpful way of waiting for EDJob to be finished
# TODO Fix this in EDJob some time
while (True):
status = edJob.getStatus()
if (status is None):
time.sleep(0.2) # 200 ms
continue
if ("failure" == status):
raise Exception("EDJob failed! ")
if ("success" == status):
break
ret = edJob.getDataOutput()
return str(ret)
def runMXv1Pipeline():
strLogFileName = os.path.join(returnWorkingDirectory(), "wsgi-server.log")
EDVerbose.setLogFileName(strLogFileName)
strInput = str(request['wsgi.input'].read(int(request['CONTENT_LENGTH'])))
if strInput:
# Take the parameters string, split off the title and run the bash script to generate the input char. XML
listParams = shlex.split(strInput)
strComments = listParams[0] # the 1st item
strShortComments = listParams[1] # the 2nd item
strWorkingDir = listParams[2] # the 3rd item
strHTMLResultDir = listParams[3] # the 4th item
os.chdir(strWorkingDir)
strParamString = " ".join(
listParams[4:]) # all but the first four items
edPluginMxv1ParamsToXML = EDFactoryPluginStatic.loadPlugin(
'EDPluginMxv1ParamsToXMLv1_0')
edPluginMxv1ParamsToXML.setDataInput(XSDataString(strParamString),
"paramString")
edPluginMxv1ParamsToXML.executeSynchronous()
xsDataFile = edPluginMxv1ParamsToXML.getDataOutput()
# Read the XML and parse it into an object hierarchy
strXMLFile = xsDataFile.getPath().getValue()
f = open(strXMLFile, 'r')
xml = f.read()
f.close()
xsDataInputCharacterisation = XSDataInputCharacterisation.parseString(
xml)
# Run the MXv1 application pipeline
edApplicationMXv1Characterisation = EDApplicationMXv1Characterisation(_strPluginName="EDPluginControlInterfacev1_2", \
_strConfigurationFileName=strConfigurationFilePath, \
_xsDataInputCharacterisation=xsDataInputCharacterisation, \
_strComments=strComments, \
_strShortComments=strShortComments)
edApplicationMXv1Characterisation.execute()
# Run the EDNA2HTML generator on the output from the MXv1 application
edPluginExecOutputHTML = EDFactoryPluginStatic.loadPlugin(
'EDPluginExecOutputHTMLv1_0')
edPluginExecOutputHTML.setDataInput(XSDataString(strComments), "title")
strWorkingDir = os.path.join(
strWorkingDir, edApplicationMXv1Characterisation.getWorkingDir())
edPluginExecOutputHTML.setDataInput(XSDataString(strWorkingDir),
"workingDir")
#strBaseDir = os.path.join(strHTMLResultDir, "edna")
#edPluginExecOutputHTML.setDataInput(XSDataString(strBaseDir), "basename")
edPluginExecOutputHTML.setDataInput(XSDataString(strHTMLResultDir),
"basename")
edPluginExecOutputHTML.executeSynchronous()
strPathToHTMLFile = ""
if (edPluginExecOutputHTML.hasDataOutput("htmlFile")):
strPathToHTMLFile = edPluginExecOutputHTML.getDataOutput(
"htmlFile")[0].getPath().getValue()
else:
EDVerbose.ERROR(
"edna-mxv1-wsgi-server: edPluginExecOutputHTML has no dataOutput htmlFile!"
)
if strPathToHTMLFile == "":
EDVerbose.ERROR("edna-mxv1-wsgi-server: Returning empty string")
return strPathToHTMLFile
else:
return strInput
