def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlXdsBest.preProcess")
self._xds = self.loadPlugin('EDPluginExecMinimalXdsv1_0')
# save the root path (where the initial xds.inp is) for later use
self.root_dir = os.path.abspath(os.path.dirname(self.dataInput.input_file.value))
# let's begin by copying the input file to avoid clobbering it
shutil.copy(self.dataInput.input_file.value,
self.getWorkingDirectory())
self.real_input_file = os.path.join(self.getWorkingDirectory(),
os.path.basename(self.dataInput.input_file.value))
# update the keywords
self.parsed_config = parse_xds_file(self.real_input_file)
di = self.dataInput
unit_cell_constants = '{0:.2f} {1:.2f} {2:.2f} {3:.2f} {4:.2f} {5:.2f}'.format(
di.unit_cell_a.value,
di.unit_cell_b.value,
di.unit_cell_c.value,
di.unit_cell_alpha.value,
di.unit_cell_beta.value,
di.unit_cell_gamma.value)
sg = int(di.space_group.value)
self.parsed_config['UNIT_CELL_CONSTANTS='] = unit_cell_constants
self.parsed_config['SPACE_GROUP_NUMBER='] = sg
# to avoid any problem let's also make the image template
# absolute as well. The underlying XDS template will take care
# of creating the links in its dir
imtemplate = self.parsed_config['NAME_TEMPLATE_OF_DATA_FRAMES='][0]
basedir = os.path.abspath(os.path.dirname(self.dataInput.input_file.value))
newpath = os.path.join(basedir, imtemplate)
self.parsed_config['NAME_TEMPLATE_OF_DATA_FRAMES='] = newpath
# Make the [XY]-GEO_CORR paths absolute
if 'X-GEO_CORR=' in self.parsed_config:
xgeo = os.path.abspath(os.path.join(self.root_dir,
self.parsed_config['X-GEO_CORR='][0]))
if not os.path.exists(xgeo):
self.DEBUG('geometry file {0} does not exist, removing'.format(xgeo))
del self.parsed_config['X-GEO_CORR=']
else:
self.parsed_config['X-GEO_CORR='] = xgeo
if 'Y-GEO_CORR=' in self.parsed_config:
ygeo = os.path.abspath(os.path.join(self.root_dir,
self.parsed_config['Y-GEO_CORR='][0]))
if not os.path.exists(ygeo):
self.DEBUG('geometry file {0} does not exist, removing'.format(ygeo))
del self.parsed_config['Y-GEO_CORR=']
else:
self.parsed_config['Y-GEO_CORR='] = ygeo
dump_xds_file(self.real_input_file, self.parsed_config)
# create the input data model for the XDS plugin
input_dm = XSDataMinimalXdsIn()
input_dm.input_file = XSDataString(self.real_input_file)
self._xds.dataInput = input_dm
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlXdsBest.process")
self._xds.executeSynchronous()
expected = os.path.join(self._xds.getWorkingDirectory(), 'XDS_ASCII.HKL')
if not os.path.exists(expected):
# Try to re-run with JOB = DEFPIX INTEGRATE CORRECT
self.parsed_config["JOB="] = "DEFPIX INTEGRATE CORRECT"
self._xds2 = self.loadPlugin('EDPluginExecMinimalXdsv1_0')
self._xds2.setWorkingDirectory(self._xds.getWorkingDirectory())
dump_xds_file(self.real_input_file, self.parsed_config)
input_dm2 = XSDataMinimalXdsIn()
input_dm2.input_file = XSDataString(self.real_input_file)
self._xds2.dataInput = input_dm2
self._xds2.executeSynchronous()
def process(self, _edObject=None):
EDPluginControl.process(self)
self.DEBUG("EDPluginControlXdsBest.process")
self._xds.executeSynchronous()
expected = os.path.join(self._xds.getWorkingDirectory(),
'XDS_ASCII.HKL')
if not os.path.exists(expected):
# Try to re-run with JOB = DEFPIX INTEGRATE CORRECT
self.parsed_config["JOB="] = "DEFPIX INTEGRATE CORRECT"
self._xds2 = self.loadPlugin('EDPluginExecMinimalXdsv1_0')
self._xds2.setWorkingDirectory(self._xds.getWorkingDirectory())
dump_xds_file(self.real_input_file, self.parsed_config)
input_dm2 = XSDataMinimalXdsIn()
input_dm2.input_file = XSDataString(self.real_input_file)
self._xds2.dataInput = input_dm2
self._xds2.executeSynchronous()
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginXDSGeneratev1_0.preProcess")
self.xds_anom = self.loadPlugin('EDPluginExecMinimalXdsv1_0')
self.xds_noanom = self.loadPlugin('EDPluginExecMinimalXdsv1_0')
path = os.path.abspath(self.dataInput.previous_run_dir.value)
# The MinimalXds plugin takes care of creating determining the
# real images directory and creating a symlink to it so we
# only need to update the NAMED_TEMPLATE_OF_DATA_FILES keyword
# to not be relative anymore. We'll copy it to our own dir
# beforehand to avoid clobbering it
xdsinp = os.path.join(path, 'XDS.INP')
new_xdsinp = os.path.join(self.getWorkingDirectory(), 'XDS.INP')
copyfile(xdsinp, new_xdsinp)
parsed_config = parse_xds_file(new_xdsinp)
file_template = parsed_config['NAME_TEMPLATE_OF_DATA_FRAMES='][0]
parsed_config['NAME_TEMPLATE_OF_DATA_FRAMES='] = os.path.abspath(os.path.join(path, file_template))
dump_xds_file(new_xdsinp, parsed_config)
# create the data inputs now we know the files are here
input_anom = XSDataMinimalXdsIn()
input_anom.input_file = XSDataString(new_xdsinp)
input_anom.friedels_law = XSDataBoolean(False)
input_anom.job = XSDataString('CORRECT')
input_anom.resolution = self.dataInput.resolution
input_anom.resolution_range = [XSDataDouble(60), self.dataInput.resolution]
input_anom.spacegroup = self.dataInput.spacegroup
input_anom.unit_cell = self.dataInput.unit_cell
self.xds_anom.dataInput = input_anom
input_noanom = XSDataMinimalXdsIn()
input_noanom.input_file = XSDataString(new_xdsinp)
input_noanom.friedels_law = XSDataBoolean(True)
input_noanom.job = XSDataString('CORRECT')
input_noanom.resolution_range = [XSDataDouble(60), self.dataInput.resolution]
input_noanom.spacegroup = self.dataInput.spacegroup
input_noanom.unit_cell = self.dataInput.unit_cell
self.xds_noanom.dataInput = input_noanom
xds_anom_dir = os.path.abspath(self.xds_anom.getWorkingDirectory())
xds_noanom_dir = os.path.abspath(self.xds_noanom.getWorkingDirectory())
# let's make some links!
for f in self._to_link:
os.symlink(f, os.path.join(xds_anom_dir, os.path.basename(f)))
os.symlink(f, os.path.join(xds_noanom_dir, os.path.basename(f)))
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlXdsBest.preProcess")
self._xds = self.loadPlugin('EDPluginExecMinimalXdsv1_0')
# save the root path (where the initial xds.inp is) for later use
self.root_dir = os.path.abspath(
os.path.dirname(self.dataInput.input_file.value))
# let's begin by copying the input file to avoid clobbering it
shutil.copy(self.dataInput.input_file.value,
self.getWorkingDirectory())
self.real_input_file = os.path.join(
self.getWorkingDirectory(),
os.path.basename(self.dataInput.input_file.value))
# update the keywords
self.parsed_config = parse_xds_file(self.real_input_file)
di = self.dataInput
unit_cell_constants = '{0:.2f} {1:.2f} {2:.2f} {3:.2f} {4:.2f} {5:.2f}'.format(
di.unit_cell_a.value, di.unit_cell_b.value, di.unit_cell_c.value,
di.unit_cell_alpha.value, di.unit_cell_beta.value,
di.unit_cell_gamma.value)
sg = int(di.space_group.value)
self.parsed_config['UNIT_CELL_CONSTANTS='] = unit_cell_constants
self.parsed_config['SPACE_GROUP_NUMBER='] = sg
# to avoid any problem let's also make the image template
# absolute as well. The underlying XDS template will take care
# of creating the links in its dir
imtemplate = self.parsed_config['NAME_TEMPLATE_OF_DATA_FRAMES='][0]
basedir = os.path.abspath(
os.path.dirname(self.dataInput.input_file.value))
newpath = os.path.join(basedir, imtemplate)
self.parsed_config['NAME_TEMPLATE_OF_DATA_FRAMES='] = newpath
# Make the [XY]-GEO_CORR paths absolute
if 'X-GEO_CORR=' in self.parsed_config:
xgeo = os.path.abspath(
os.path.join(self.root_dir,
self.parsed_config['X-GEO_CORR='][0]))
if not os.path.exists(xgeo):
self.DEBUG(
'geometry file {0} does not exist, removing'.format(xgeo))
del self.parsed_config['X-GEO_CORR=']
else:
self.parsed_config['X-GEO_CORR='] = xgeo
if 'Y-GEO_CORR=' in self.parsed_config:
ygeo = os.path.abspath(
os.path.join(self.root_dir,
self.parsed_config['Y-GEO_CORR='][0]))
if not os.path.exists(ygeo):
self.DEBUG(
'geometry file {0} does not exist, removing'.format(ygeo))
del self.parsed_config['Y-GEO_CORR=']
else:
self.parsed_config['Y-GEO_CORR='] = ygeo
dump_xds_file(self.real_input_file, self.parsed_config)
# create the input data model for the XDS plugin
input_dm = XSDataMinimalXdsIn()
input_dm.input_file = XSDataString(self.real_input_file)
self._xds.dataInput = input_dm
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 preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginXDSGeneratev1_0.preProcess")
if self.dataInput.doAnomAndNonanom is not None:
if self.dataInput.doAnomAndNonanom.value:
self.doAnomAndNonanom = True
else:
self.doAnomAndNonanom = False
self.xds_anom = self.loadPlugin('EDPluginExecMinimalXdsv1_0')
if self.doAnomAndNonanom:
self.xds_noanom = self.loadPlugin('EDPluginExecMinimalXdsv1_0')
path = os.path.abspath(self.dataInput.previous_run_dir.value)
# The MinimalXds plugin takes care of creating determining the
# real images directory and creating a symlink to it so we
# only need to update the NAMED_TEMPLATE_OF_DATA_FILES keyword
# to not be relative anymore. We'll copy it to our own dir
# beforehand to avoid clobbering it
xdsinp = os.path.join(path, 'XDS.INP')
new_xdsinp = os.path.join(self.getWorkingDirectory(), 'XDS.INP')
copyfile(xdsinp, new_xdsinp)
parsed_config = parse_xds_file(new_xdsinp)
file_template = parsed_config['NAME_TEMPLATE_OF_DATA_FRAMES='][0]
parsed_config['NAME_TEMPLATE_OF_DATA_FRAMES='] = os.path.abspath(
os.path.join(path, file_template))
dump_xds_file(new_xdsinp, parsed_config)
# create the data inputs now we know the files are here
input_anom = XSDataMinimalXdsIn()
input_anom.input_file = XSDataString(new_xdsinp)
input_anom.friedels_law = XSDataBoolean(False)
input_anom.job = XSDataString('CORRECT')
input_anom.resolution = self.dataInput.resolution
input_anom.resolution_range = [
XSDataDouble(60), self.dataInput.resolution
]
input_anom.spacegroup = self.dataInput.spacegroup
input_anom.unit_cell = self.dataInput.unit_cell
self.xds_anom.dataInput = input_anom
xds_anom_dir = os.path.abspath(self.xds_anom.getWorkingDirectory())
if self.doAnomAndNonanom:
input_noanom = XSDataMinimalXdsIn()
input_noanom.input_file = XSDataString(new_xdsinp)
input_noanom.friedels_law = XSDataBoolean(True)
input_noanom.job = XSDataString('CORRECT')
input_noanom.resolution_range = [
XSDataDouble(60), self.dataInput.resolution
]
input_noanom.spacegroup = self.dataInput.spacegroup
input_noanom.unit_cell = self.dataInput.unit_cell
self.xds_noanom.dataInput = input_noanom
xds_noanom_dir = os.path.abspath(
self.xds_noanom.getWorkingDirectory())
# let's make some links!
for f in self._to_link:
os.symlink(f, os.path.join(xds_anom_dir, os.path.basename(f)))
if self.doAnomAndNonanom:
os.symlink(f, os.path.join(xds_noanom_dir,
os.path.basename(f)))
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
