def _copy_collection_by_id(collection_id, staging):
setup(blconfig.get_database(staging=staging))
c = Collection(collection_id)
c.reload()
setup(blconfig.get_database(staging=not staging))
newc = Collection()
newc.__dict__ = c.__dict__
newc._id = None
newc.save()
return newc.dbref
def copy_all_collections_from_epn_to_staging(epn):
setup(blconfig.get_database(staging=False))
from processingDB import VisitStats
v = VisitStats()
(all_coll, all_proc) = v.get_epn_info(epn)
iddict = {}
for coll in all_coll:
#print "copying %s to staging..." % coll['_id']
oldid = str(coll['_id'])
newid = copy_to_staging_by_id(coll['_id'])
iddict[oldid] = newid
return iddict
def process(self, **kwargs):
if kwargs['collection_id']:
coll = Collection(kwargs['collection_id'])
else:
setup(blconfig.get_database())
proc = Processing(kwargs['dataset_id'])
coll = Collection(str(proc.collection_id.id))
try:
cryo_temp = coll.cryo_temperature
except AttributeError:
cryo_temp = None
try:
crystal_in_monochromator = coll.crystal_in_monochromator
except AttributeError:
crystal_in_monochromator = None
try:
sample_desc = coll.sample_desc
except AttributeError:
sample_desc = 'user input'
try:
sample_colour = coll.sample_colour
except AttributeError:
sample_colour = 'user input'
try:
sample_size_min = coll.sample_size_min
except AttributeError:
sample_size_min = 'user input'
try:
sample_size_mid = coll.sample_size_mid
except AttributeError:
sample_size_mid = 'user input'
try:
sample_size_max = coll.sample_size_max
except AttributeError:
sample_size_max = 'user input'
write_template_file(self.project_dir, coll.beamline, coll.detector_type, coll.energy, cryo_temp, crystal_in_monochromator, sample_desc, sample_colour, sample_size_min, sample_size_mid, sample_size_max)
import logbook
from itertools import chain
from modules.base import ReturnOptions
logger = logbook.Logger('MAIN')
logbook.StreamHandler(sys.stdout).push_application()
logbook.set_datetime_format("local")
# load modules
import pipelines
from beamline import variables as blconfig
from processing.models import setup, Dataset, Screening, Collection
setup(blconfig.get_database(staging=IS_STAGING))
parser = argparse.ArgumentParser()
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('--collection_id')
group.add_argument('--dataset_id')
parser.add_argument('--data_dir')
parser.add_argument('--output_dir')
parser.add_argument('--processing_dir',
help="Location of previously run processing directory")
parser.add_argument('--dry_run',
help='Show the pipeline without actually running it')
# add parser arguments from all classes inside the pipelines
for clz in set([obj.__class__
for obj in chain(*pipelines.pipelines.values())]):
def _copy_processing_by_obj(processing, staging):
setup(blconfig.get_database(staging=staging))
newp = Processing()
newp.__dict__ = processing
newp._id = None
newp.save()
def get_retrigger_dir(dataset_id):
setup(blconfig.get_database())
dataset = Dataset(dataset_id)
collection_id = dataset.collection_id.id
PI = Collection(collection_id).PI
return "/data/%(EPN)s/home/%(PI)s/auto" % {"EPN": blconfig.EPN, "PI": PI}