def command(self):
app = self.load_wsgi_app()
storage = QLStorageSource(app.config)
if len(self.args) < 2:
print self.__class__.usage
return
for i in range(0,len(self.args)-1):
plate_id = int(self.args[i])
plate = dbplate_tree(plate_id)
try:
plate_path = storage.plate_path(plate)
except Exception, e:
print "Could not read plate: %s" % plate_id
continue
qlplate = get_plate(plate_path)
if not qlplate:
raise ValueError, "Could not read plate: %s" % plate_path
else:
print "Processing %s" % plate_path
try:
from qtools.lib.metrics import DEFAULT_CNV_CALC, compute_metric_foreach_qlwell
plate_metrics = plate.metrics[0]
compute_metric_foreach_qlwell(qlplate, plate_metrics, DEFAULT_CNV_CALC)
except Exception, e:
import sys, traceback
traceback.print_exc(file=sys.stdout)
Session.rollback()
return
def command(self):
app = self.load_wsgi_app()
# enforce config.ini
if len(self.args) < 2:
raise ValueError, self.__class__.usage
plate_id = int(self.args[0])
plate = dbplate_tree(plate_id)
if not plate:
raise ValueError, "Invalid plate id: %s" % plate_id
storage = QLStorageSource(app.config)
# for now, no reprocessing.
plate_path = storage.plate_path(plate)
qlplate = get_plate(plate_path)
if not qlplate:
raise ValueError, "Could not read plate: %s" % plate_path
try:
plate_metrics = plate.metrics[0]
self.process_plate( qlplate, plate_metrics)
except Exception, e:
import sys, traceback
traceback.print_exc(file=sys.stdout)
Session.rollback()
return
def command(self):
app = self.load_wsgi_app()
print "Clearing NEB buffer tables..."
# make this reversible...
neb = Session.query(Vendor).filter_by(name='NEB').first()
if neb:
enzymes = neb.enzymes
for enz in enzymes:
Session.delete(enz)
neb.enzymes = []
Session.commit()
# now go with the vendors (question: is it vendor enzyme or enzyme
# in general subject to methylation)
source = NEBEnzymeSource()
if not neb:
neb = Vendor(name="NEB", website="http://www.neb.com")
Session.add(neb)
Session.commit()
try:
for name, page_uri in source.iter_restriction_enzymes():
print "Processing %s..." % name
enz = Session.query(Enzyme).filter_by(name=name).first()
if not enz:
enz = Enzyme(name=name)
Session.add(enz)
details = source.enzyme_details(name, page_uri)
if details:
enz.cutseq = details['sequence']
enz.methylation = details['methylation_sensitivity']
buf = Session.query(Buffer).filter_by(name=details['buffer']).first()
if not buf:
buf = Buffer(name=details['buffer'])
Session.add(buf)
ve = VendorEnzyme(enzyme=enz, vendor=neb, buffer=buf)
ve.unit_cost_1 = details.get('unit_cost_1', None)
ve.unit_cost_2 = details.get('unit_cost_2', None)
ve.unit_serial_1 = details.get('unit_serial_1', None)
ve.unit_serial_2 = details.get('unit_serial_2', None)
ve.vendor_serial = details.get('vendor_serial', None)
if ve.unit_cost_1 is not None:
Session.add(ve)
# save per enzyme, interruption should be logged
Session.commit()
except IOError, e:
Session.rollback()
print "Could not communicate with NEB server"
def process_plates(self, app, analysis_group, reprocess_config):
storage = QLStorageSource(app.config)
plates = analysis_group.plates
for plate in plates:
pms = [pm for pm in plate.metrics if pm.reprocess_config_id == reprocess_config.id]
if not pms:
print "Cannot find analysis group for plate %s" % plate.id
else:
pm = pms[0]
dbplate = dbplate_tree(plate.id)
if reprocess_config:
data_root = app.config['qlb.reprocess_root']
storage = QLPReprocessedFileSource(data_root, reprocess_config)
else:
storage = QLStorageSource(app.config)
try:
if reprocess_config:
plate_path = storage.full_path(analysis_group, dbplate)
else:
plate_path = storage.plate_path(dbplate)
except Exception, e:
print "Could not read plate: %s" % plate.id
continue
qlplate = get_plate(plate_path)
if not qlplate:
raise ValueError, "Could not read plate: %s" % plate_path
else:
print "Processing %s" % plate_path
try:
self.backfill_plate(qlplate, pm)
Session.commit()
except Exception, e:
print "Could not process plate %s" % dbplate.id
import sys, traceback
traceback.print_exc(file=sys.stdout)
Session.rollback()
continue
