def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlRunXdsv1_0.process")
# First run is vanilla without any modification
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
self.first_run.dataInput = params
self.first_run.executeSynchronous()
EDVerbose.DEBUG('first run completed...')
if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.first_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# second run w/ JOB set to DEFPIX INTEGRATE CORRECT
self.second_run = self.loadPlugin(self.controlled_plugin_name)
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.jobs = 'DEFPIX INTEGRATE CORRECT'
self.second_run.dataInput = params
self.second_run.executeSynchronous()
EDVerbose.DEBUG('second run completed')
if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.second_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# third run with JOB set to ALL and mxaprocs = 4 and maxjobs = 1
self.third_run = self.loadPlugin(self.controlled_plugin_name)
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.jobs = 'ALL'
params.maxprocs = 4
params.maxjobs = 1
self.third_run.dataInput = params
self.third_run.executeSynchronous()
EDVerbose.DEBUG('third run completed')
if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.third_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# final run with parallelism like 3 but JOB like 2
self.final_run = self.loadPlugin(self.controlled_plugin_name)
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.jobs = 'DEFPIX INTEGRATE CORRECT'
params.maxprocs = 4
params.maxjobs = 1
self.final_run.dataInput = params
self.final_run.executeSynchronous()
EDVerbose.DEBUG('final run completed')
if self.final_run.dataOutput is not None and self.final_run.dataOutput.succeeded:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.final_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# all runs failed so bail out ...
strErrorMessage = "All XDS run failed"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
else:
# use the xds parser plugin to parse the xds output file...
parser = self.loadPlugin("EDPluginParseXdsOutputv1_0")
wd = self.successful_run.getWorkingDirectory()
parser_input = XSDataXdsOutputFile()
correct_lp_path = XSDataFile()
correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP'))
parser_input.correct_lp = correct_lp_path
gxparm_path = os.path.join(wd, 'GXPARM.XDS')
if os.path.isfile(gxparm_path):
gxparm = XSDataFile()
gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS'))
parser_input.gxparm = gxparm
parser.dataInput = parser_input
parser.executeSynchronous()
if parser.isFailure():
# that should not happen
strErrorMessage = "Parser failure in control run XDS"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
self.dataOutput = parser.dataOutput
def process(self, _edObject = None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlRunXdsFastProc.process")
# First run is vanilla without any modification
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
self.first_run.dataInput = params
self.first_run.executeSynchronous()
EDVerbose.DEBUG('first run completed...')
if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.first_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.second_run = self.loadPlugin(self.controlled_plugin_name)
self.DEBUG('retrying with increased SPOT_RANGE')
self.DEBUG('copying previously generated files to the new plugin dir')
copy_xds_files(self.first_run.getWorkingDirectory(),
self.second_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# increase all the spot ranges end by 20, constrained to
# the data range upper limit
spot_range = list()
for srange in self.spot_range:
range_begin = srange[0]
range_end = srange[1] + 20
if range_end > self.end_image_no:
self.DEBUG('End of range {0} would be past the last image {1}'.format(range_end,
self.end_image_no))
range_end = self.end_image_no
self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(srange, range_begin, range_end))
r = XSDataRange(begin=range_begin, end=range_end)
spot_range.append(r)
params.spot_range = spot_range
self.second_run.dataInput = params
self.second_run.executeSynchronous()
EDVerbose.DEBUG('second run completed')
if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.second_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.third_run = self.loadPlugin(self.controlled_plugin_name)
self.DEBUG('retrying with increased SPOT_RANGE')
self.DEBUG('copying previously generated files to the new plugin dir')
copy_xds_files(self.second_run.getWorkingDirectory(),
self.third_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
spot_range = list()
for srange in self.spot_range:
range_begin = srange[0]
range_end = srange[1] + 40
if range_end > self.end_image_no:
self.DEBUG('End of range {0} would be past the last image {1}'.format(range_end,
self.end_image_no))
range_end = self.end_image_no
self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(srange, range_begin, range_end))
r = XSDataRange(begin=range_begin, end=range_end)
spot_range.append(r)
params.spot_range = spot_range
self.third_run.dataInput = params
self.third_run.executeSynchronous()
EDVerbose.DEBUG('third run completed')
if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.third_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# all runs failed so bail out ...
self.setFailure()
else:
# use the xds parser plugin to parse the xds output file...
parser = self.loadPlugin("EDPluginParseXdsOutput")
wd = self.successful_run.getWorkingDirectory()
parser_input = XSDataXdsOutputFile()
correct_lp_path = XSDataFile()
correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP'))
parser_input.correct_lp = correct_lp_path
gxparm_path = os.path.join(wd, 'GXPARM.XDS')
if os.path.isfile(gxparm_path):
gxparm = XSDataFile()
gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS'))
parser_input.gxparm = gxparm
parser.dataInput = parser_input
parser.executeSynchronous()
if parser.isFailure():
# that should not happen
self.setFailure()
return
self.dataOutput = parser.dataOutput
def process(self, _edObject = None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlRunXds.process")
# First run is vanilla without any modification
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
self.first_run.dataInput = params
self.first_run.executeSynchronous()
EDVerbose.DEBUG('first run completed...')
if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.first_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# second run w/ JOB set to DEFPIX INTEGRATE CORRECT
self.second_run = self.loadPlugin(self.controlled_plugin_name)
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.jobs = 'DEFPIX INTEGRATE CORRECT'
self.second_run.dataInput = params
self.second_run.executeSynchronous()
EDVerbose.DEBUG('second run completed')
if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.second_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# third run with JOB set to ALL and mxaprocs = 4 and maxjobs = 1
self.third_run = self.loadPlugin(self.controlled_plugin_name)
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.jobs = 'ALL'
params.maxprocs = 4
params.maxjobs = 1
self.third_run.dataInput = params
self.third_run.executeSynchronous()
EDVerbose.DEBUG('third run completed')
if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.third_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# final run with parallelism like 3 but JOB like 2
self.final_run = self.loadPlugin(self.controlled_plugin_name)
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.jobs = 'DEFPIX INTEGRATE CORRECT'
params.maxprocs = 4
params.maxjobs = 1
self.final_run.dataInput = params
self.final_run.executeSynchronous()
EDVerbose.DEBUG('final run completed')
if self.final_run.dataOutput is not None and self.final_run.dataOutput.succeeded:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.final_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# all runs failed so bail out ...
self.setFailure()
else:
# use the xds parser plugin to parse the xds output file...
parser = self.loadPlugin("EDPluginParseXdsOutput")
wd = self.successful_run.getWorkingDirectory()
parser_input = XSDataXdsOutputFile()
correct_lp_path = XSDataFile()
correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP'))
parser_input.correct_lp = correct_lp_path
gxparm_path = os.path.join(wd, 'GXPARM.XDS')
if os.path.isfile(gxparm_path):
gxparm = XSDataFile()
gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS'))
parser_input.gxparm = gxparm
parser.dataInput = parser_input
parser.executeSynchronous()
if parser.isFailure():
# that should not happen
self.setFailure()
return
self.dataOutput = parser.dataOutput
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlRunXdsFastProcv1_0.process")
# First run is vanilla without any modification
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# Fix for 'SPOT_RANGE 0 100' problem
for srange in self.spot_range:
if srange[0] > 0:
xsDataRange = XSDataRange()
xsDataRange.begin = srange[0]
xsDataRange.end = srange[1]
params.addSpot_range(xsDataRange)
# Gleb on Mon Aug 4 18:54:36 CEST 2014: set jobs parameters in order to prevent
# params.job = XSDataString('XYCORR INIT COLSPOT IDXREF')
self.first_run.dataInput = params
self.first_run.executeSynchronous()
self.retrieveFailureMessages(self.first_run, "First XDS run")
EDVerbose.DEBUG('first run completed...')
if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.first_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.second_run = self.loadPlugin(self.controlled_plugin_name)
self.screen('Retrying with increased SPOT_RANGE')
self.DEBUG('copying previously generated files to the new plugin dir')
copy_xds_files(self.first_run.getWorkingDirectory(),
self.second_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
# params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# Extended spot range
if self.end_image_no <= 300:
# All data as spot range
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = 1
xsDataRangeLimited.end = self.end_image_no
params.addSpot_range(xsDataRangeLimited)
else:
# Start spot range
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = 1
xsDataRangeLimited.end = 100
params.addSpot_range(xsDataRangeLimited)
# Start spot range
middleImageNumber = int(self.end_image_no / 2)
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = middleImageNumber - 49
xsDataRangeLimited.end = middleImageNumber + 50
params.addSpot_range(xsDataRangeLimited)
# End spot range
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = self.end_image_no - 99
xsDataRangeLimited.end = self.end_image_no
params.addSpot_range(xsDataRangeLimited)
self.second_run.dataInput = params
self.second_run.executeSynchronous()
self.retrieveFailureMessages(self.second_run, "Second XDS run")
EDVerbose.DEBUG('second run completed')
if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.second_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.third_run = self.loadPlugin(self.controlled_plugin_name)
self.screen('Retrying with reduced SPOT_RANGE')
self.DEBUG('copying previously generated files to the new plugin dir')
copy_xds_files(self.first_run.getWorkingDirectory(),
self.third_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
# params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# Limited spot range: 1 to 20 or max no data points
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = 1
xsDataRangeLimited.end = 20 if self.end_image_no > 20 else self.end_image_no
params.addSpot_range(xsDataRangeLimited)
self.third_run.dataInput = params
self.third_run.executeSynchronous()
self.retrieveFailureMessages(self.third_run, "Second XDS run")
EDVerbose.DEBUG('second run completed')
if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.third_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# all runs failed so bail out ...
strErrorMessage = "All three XDS runs failed"
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
else:
# use the xds parser plugin to parse the xds output file...
parser = self.loadPlugin("EDPluginParseXdsOutputv1_0")
wd = self.successful_run.getWorkingDirectory()
parser_input = XSDataXdsOutputFile()
correct_lp_path = XSDataFile()
correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP'))
parser_input.correct_lp = correct_lp_path
gxparm_path = os.path.join(wd, 'GXPARM.XDS')
if os.path.isfile(gxparm_path):
gxparm = XSDataFile()
gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS'))
parser_input.gxparm = gxparm
parser.dataInput = parser_input
parser.executeSynchronous()
if parser.isFailure():
# that should not happen
strErrorMessage = "Parser failure in XDS fast proc"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
self.dataOutput = parser.dataOutput
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlRunXdsFastProc.process")
# First run is vanilla without any modification
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
self.first_run.dataInput = params
self.first_run.executeSynchronous()
EDVerbose.DEBUG('first run completed...')
if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.first_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.second_run = self.loadPlugin(self.controlled_plugin_name)
self.DEBUG('retrying with increased SPOT_RANGE')
self.DEBUG(
'copying previously generated files to the new plugin dir')
copy_xds_files(self.first_run.getWorkingDirectory(),
self.second_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# increase all the spot ranges end by 20, constrained to
# the data range upper limit
spot_range = list()
for srange in self.spot_range:
range_begin = srange[0]
range_end = srange[1] + 20
if range_end > self.end_image_no:
self.DEBUG(
'End of range {0} would be past the last image {1}'.
format(range_end, self.end_image_no))
range_end = self.end_image_no
self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(
srange, range_begin, range_end))
r = XSDataRange(begin=range_begin, end=range_end)
spot_range.append(r)
params.spot_range = spot_range
self.second_run.dataInput = params
self.second_run.executeSynchronous()
EDVerbose.DEBUG('second run completed')
if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.second_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.third_run = self.loadPlugin(self.controlled_plugin_name)
self.DEBUG('retrying with increased SPOT_RANGE')
self.DEBUG(
'copying previously generated files to the new plugin dir')
copy_xds_files(self.second_run.getWorkingDirectory(),
self.third_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
spot_range = list()
for srange in self.spot_range:
range_begin = srange[0]
range_end = srange[1] + 40
if range_end > self.end_image_no:
self.DEBUG(
'End of range {0} would be past the last image {1}'.
format(range_end, self.end_image_no))
range_end = self.end_image_no
self.DEBUG('Changing spot range {0} to [{1} {2}]'.format(
srange, range_begin, range_end))
r = XSDataRange(begin=range_begin, end=range_end)
spot_range.append(r)
params.spot_range = spot_range
self.third_run.dataInput = params
self.third_run.executeSynchronous()
EDVerbose.DEBUG('third run completed')
if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.third_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# all runs failed so bail out ...
self.setFailure()
else:
# use the xds parser plugin to parse the xds output file...
parser = self.loadPlugin("EDPluginParseXdsOutput")
wd = self.successful_run.getWorkingDirectory()
parser_input = XSDataXdsOutputFile()
correct_lp_path = XSDataFile()
correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP'))
parser_input.correct_lp = correct_lp_path
gxparm_path = os.path.join(wd, 'GXPARM.XDS')
if os.path.isfile(gxparm_path):
gxparm = XSDataFile()
gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS'))
parser_input.gxparm = gxparm
parser.dataInput = parser_input
parser.executeSynchronous()
if parser.isFailure():
# that should not happen
self.setFailure()
return
self.dataOutput = parser.dataOutput
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlRunXdsFastProcv1_0.process")
# First run is vanilla without any modification
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
params.start_image = self.dataInput.start_image
params.end_image = self.dataInput.end_image
# Fix for 'SPOT_RANGE 0 100' problem
for srange in self.spot_range:
if srange[0] > 0:
xsDataRange = XSDataRange()
xsDataRange.begin = srange[0]
xsDataRange.end = srange[1]
params.addSpot_range(xsDataRange)
# Gleb on Mon Aug 4 18:54:36 CEST 2014: set jobs parameters in order to prevent
# params.job = XSDataString('XYCORR INIT COLSPOT IDXREF')
self.first_run.dataInput = params
self.first_run.executeSynchronous()
self.retrieveFailureMessages(self.first_run, "First XDS run")
EDVerbose.DEBUG('first run completed...')
if self.first_run.dataOutput is not None and self.first_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.first_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.second_run = self.loadPlugin(self.controlled_plugin_name)
self.screen('Retrying with increased SPOT_RANGE')
self.DEBUG(
'copying previously generated files to the new plugin dir')
copy_xds_files(self.first_run.getWorkingDirectory(),
self.second_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
# params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# Extended spot range
if self.end_image_no - self.start_image_no < 300:
# All data as spot range
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = self.start_image_no
xsDataRangeLimited.end = self.end_image_no
params.addSpot_range(xsDataRangeLimited)
else:
# Start spot range
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = self.start_image_no
xsDataRangeLimited.end = self.start_image_no + 99
params.addSpot_range(xsDataRangeLimited)
# Start spot range
middleImageNumber = self.start_image_no + int(
self.end_image_no / 2) - 1
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = middleImageNumber - 49
xsDataRangeLimited.end = middleImageNumber + 50
params.addSpot_range(xsDataRangeLimited)
# End spot range
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = self.end_image_no - 99
xsDataRangeLimited.end = self.end_image_no
params.addSpot_range(xsDataRangeLimited)
self.second_run.dataInput = params
self.second_run.executeSynchronous()
self.retrieveFailureMessages(self.second_run, "Second XDS run")
EDVerbose.DEBUG('second run completed')
if self.second_run.dataOutput is not None and self.second_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.second_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
self.third_run = self.loadPlugin(self.controlled_plugin_name)
self.screen('Retrying with reduced SPOT_RANGE')
self.DEBUG(
'copying previously generated files to the new plugin dir')
copy_xds_files(self.first_run.getWorkingDirectory(),
self.third_run.getWorkingDirectory())
params = XSDataMinimalXdsIn()
params.input_file = self.dataInput.input_file
# params.job = XSDataString('DEFPIX INTEGRATE CORRECT')
params.spacegroup = self.dataInput.spacegroup
params.unit_cell = self.dataInput.unit_cell
# Limited spot range: 1 to 20 or max no data points
xsDataRangeLimited = XSDataRange()
xsDataRangeLimited.begin = 1
xsDataRangeLimited.end = 20 if self.end_image_no > 20 else self.end_image_no
params.addSpot_range(xsDataRangeLimited)
self.third_run.dataInput = params
self.third_run.executeSynchronous()
self.retrieveFailureMessages(self.third_run, "Second XDS run")
EDVerbose.DEBUG('second run completed')
if self.third_run.dataOutput is not None and self.third_run.dataOutput.succeeded.value:
EDVerbose.DEBUG('... and it worked')
self.successful_run = self.third_run
else:
EDVerbose.DEBUG('... and it failed')
if not self.successful_run:
# all runs failed so bail out ...
strErrorMessage = "All three XDS runs failed"
self.addErrorMessage(strErrorMessage)
self.ERROR(strErrorMessage)
self.setFailure()
else:
# use the xds parser plugin to parse the xds output file...
parser = self.loadPlugin("EDPluginParseXdsOutputv1_0")
wd = self.successful_run.getWorkingDirectory()
parser_input = XSDataXdsOutputFile()
correct_lp_path = XSDataFile()
correct_lp_path.path = XSDataString(os.path.join(wd, 'CORRECT.LP'))
parser_input.correct_lp = correct_lp_path
gxparm_path = os.path.join(wd, 'GXPARM.XDS')
if os.path.isfile(gxparm_path):
gxparm = XSDataFile()
gxparm.path = XSDataString(os.path.join(wd, 'GXPARM.XDS'))
parser_input.gxparm = gxparm
parser.dataInput = parser_input
parser.executeSynchronous()
if parser.isFailure():
# that should not happen
strErrorMessage = "Parser failure in XDS fast proc"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
return
self.dataOutput = parser.dataOutput
EDVerbose.screen('generating w/ and w/out anom finished')
log_to_ispyb([self.integration_id_anom, self.integration_id_noanom],
'Scaling',
'Successful',
'anom/noanom generation finished in {0}s'.format(self.stats['anom/noanom_generation']))
# we can now use the xds output parser on the two correct.lp
# files, w/ and w/out anom
parse_anom_input = XSDataXdsOutputFile()
parse_anom_input.correct_lp = XSDataFile()
parse_anom_input.correct_lp.path = self.generate.dataOutput.correct_lp_anom
# this one is the same as the first XDS run since they share
# the same directory
gxparm_file_anom = XSDataFile()
gxparm_file_anom.path = self.generate.dataOutput.gxparm
parse_anom_input.gxparm = gxparm_file_anom
self.parse_xds_anom.dataInput = parse_anom_input
self.parse_xds_anom.executeSynchronous()
if self.parse_xds_anom.isFailure():
EDVerbose.ERROR('parsing the xds generated w/ anom failed')
self.setFailure()
return
# now the other one w/out anom
parse_noanom_input = XSDataXdsOutputFile()
parse_noanom_input.correct_lp = XSDataFile()
parse_noanom_input.correct_lp.path = self.generate.dataOutput.correct_lp_no_anom
log_to_ispyb(
[self.integration_id_anom, self.integration_id_noanom],
'Scaling', 'Successful',
'anom/noanom generation finished in {0}s'.format(
self.stats['anom/noanom_generation']))
# we can now use the xds output parser on the two correct.lp
# files, w/ and w/out anom
parse_anom_input = XSDataXdsOutputFile()
parse_anom_input.correct_lp = XSDataFile()
parse_anom_input.correct_lp.path = self.generate.dataOutput.correct_lp_anom
# this one is the same as the first XDS run since they share
# the same directory
gxparm_file_anom = XSDataFile()
gxparm_file_anom.path = self.generate.dataOutput.gxparm
parse_anom_input.gxparm = gxparm_file_anom
self.parse_xds_anom.dataInput = parse_anom_input
self.parse_xds_anom.executeSynchronous()
if self.parse_xds_anom.isFailure():
EDVerbose.ERROR('parsing the xds generated w/ anom failed')
self.setFailure()
return
# now the other one w/out anom
parse_noanom_input = XSDataXdsOutputFile()
parse_noanom_input.correct_lp = XSDataFile()
parse_noanom_input.correct_lp.path = self.generate.dataOutput.correct_lp_no_anom
