def post_execute(self):
BaseQueueEntry.post_execute(self)
params = []
#JNtodo, disable end_multicollect for dataset less than 1, or energy scan
# Start grouped processing, get information from each collection
# and call autoproc with grouped processing option
for child in self.get_data_model().get_children():
for grand_child in child.get_children():
if isinstance(grand_child, queue_model_objects.DataCollection):
xds_dir = grand_child.acquisitions[0].path_template.xds_dir
residues = grand_child.processing_parameters.num_residues
anomalous = grand_child.processing_parameters.anomalous
space_group = grand_child.processing_parameters.space_group
cell = grand_child.processing_parameters.get_cell_str()
inverse_beam = grand_child.acquisitions[0].acquisition_parameters.inverse_beam
params.append({'collect_id': grand_child.id,
'xds_dir': xds_dir,
'residues': residues,
'anomalous' : anomalous,
'spacegroup': space_group,
'cell': cell,
'inverse_beam': inverse_beam})
try:
programs = self.beamline_setup.collect_hwobj["auto_processing"]
except IndexError:
# skip autoprocessing of the data
pass
else:
autoprocessing.start(programs, "end_multicollect", params)
self._set_background_color()
self._view.setText(1, "")
def trigger_auto_processing(
self,
process_event,
xds_dir,
EDNA_files_dir=None,
anomalous=None,
residues=200,
do_inducedraddam=False,
spacegroup=None,
cell=None,
):
# quick fix for anomalous, do_inducedraddam... passed as a string!!!
# (comes from the queue)
if isinstance(anomalous, str):
anomalous = anomalous == "True"
if isinstance(do_inducedraddam, str):
do_inducedraddam = do_inducedraddam == "True"
if isinstance(residues, str):
try:
residues = int(residues)
except Exception:
residues = 200
# residues = zero should be interpreted as if no value was provided
# use default of 200
if residues == 0:
residues = 200
processAnalyseParams = {}
processAnalyseParams["EDNA_files_dir"] = EDNA_files_dir
try:
if isinstance(xds_dir, list):
processAnalyseParams["collections_params"] = xds_dir
else:
processAnalyseParams["datacollect_id"] = self.collection_id
processAnalyseParams["xds_dir"] = xds_dir
processAnalyseParams["anomalous"] = anomalous
processAnalyseParams["residues"] = residues
processAnalyseParams["spacegroup"] = spacegroup
processAnalyseParams["cell"] = cell
except Exception as msg:
logging.getLogger().exception("DataCollect:processing: %r" % str(msg))
else:
# logging.info("AUTO PROCESSING: %s, %s, %s, %s, %s, %s, %r, %r", process_event, EDNA_files_dir, anomalous, residues, do_inducedraddam, spacegroup, cell)
try:
autoprocessing.start(
self["auto_processing"], process_event, processAnalyseParams
)
except Exception:
logging.getLogger().exception("Error starting processing")
if process_event == "after" and do_inducedraddam:
try:
autoprocessing.startInducedRadDam(processAnalyseParams)
except Exception:
logging.exception("Error starting induced rad.dam")
def trigger_auto_processing(
self,
process_event,
xds_dir,
EDNA_files_dir=None,
anomalous=None,
residues=200,
do_inducedraddam=False,
spacegroup=None,
cell=None,
):
# quick fix for anomalous, do_inducedraddam... passed as a string!!!
# (comes from the queue)
if isinstance(anomalous, types.StringType):
anomalous = anomalous == "True"
if isinstance(do_inducedraddam, types.StringType):
do_inducedraddam = do_inducedraddam == "True"
if isinstance(residues, types.StringType):
try:
residues = int(residues)
except BaseException:
residues = 200
# residues = zero should be interpreted as if no value was provided
# use default of 200
if residues == 0:
residues = 200
processAnalyseParams = {}
processAnalyseParams["EDNA_files_dir"] = EDNA_files_dir
try:
if isinstance(xds_dir, types.ListType):
processAnalyseParams["collections_params"] = xds_dir
else:
processAnalyseParams["datacollect_id"] = self.collection_id
processAnalyseParams["xds_dir"] = xds_dir
processAnalyseParams["anomalous"] = anomalous
processAnalyseParams["residues"] = residues
processAnalyseParams["spacegroup"] = spacegroup
processAnalyseParams["cell"] = cell
except Exception as msg:
logging.getLogger().exception("DataCollect:processing: %r" % str(msg))
else:
# logging.info("AUTO PROCESSING: %s, %s, %s, %s, %s, %s, %r, %r", process_event, EDNA_files_dir, anomalous, residues, do_inducedraddam, spacegroup, cell)
try:
autoprocessing.start(
self["auto_processing"], process_event, processAnalyseParams
)
except BaseException:
logging.getLogger().exception("Error starting processing")
if process_event == "after" and do_inducedraddam:
try:
autoprocessing.startInducedRadDam(processAnalyseParams)
except BaseException:
logging.exception("Error starting induced rad.dam")
processAnalyseParams["anomalous"] = anomalous
processAnalyseParams["residues"] = residues
processAnalyseParams["inverse_beam"] = inverse_beam
processAnalyseParams["spacegroup"] = spacegroup
processAnalyseParams["cell"] = cell
except Exception, msg:
logging.getLogger().exception("DataCollect:processing: %r" % msg)
else:
logging.info(
"AUTO PROCESSING: %s, %s, %s, %s, %s, %s, %r, %r",
process_event,
EDNA_files_dir,
anomalous,
residues,
inverse_beam,
do_inducedraddam,
spacegroup,
cell,
)
try:
autoprocessing.start(self["auto_processing"], process_event, processAnalyseParams)
except:
logging.getLogger().exception("Error starting processing")
if process_event == "after" and do_inducedraddam:
try:
autoprocessing.startInducedRadDam(processAnalyseParams)
except:
logging.exception("Error starting induced rad.dam")
try:
if type(xds_dir) == types.ListType:
processAnalyseParams["collections_params"] = xds_dir
else:
processAnalyseParams['datacollect_id'] = self.collection_id
processAnalyseParams['xds_dir'] = xds_dir
processAnalyseParams['anomalous'] = anomalous
processAnalyseParams['residues'] = residues
processAnalyseParams['inverse_beam'] = inverse_beam
processAnalyseParams["spacegroup"] = spacegroup
processAnalyseParams["cell"] = cell
except Exception, msg:
logging.getLogger().exception("DataCollect:processing: %r" % msg)
else:
logging.info("AUTO PROCESSING: %s, %s, %s, %s, %s, %s, %r, %r",
process_event, EDNA_files_dir, anomalous, residues,
inverse_beam, do_inducedraddam, spacegroup, cell)
try:
autoprocessing.start(self["auto_processing"], process_event,
processAnalyseParams)
except:
logging.getLogger().exception("Error starting processing")
if process_event == "after" and do_inducedraddam:
try:
autoprocessing.startInducedRadDam(processAnalyseParams)
except:
logging.exception("Error starting induced rad.dam")
