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 from_plate(self, id=None):
if not id:
abort(404)
plate = Session.query(Plate).get(id)
if not plate:
abort(404)
# ignore possibility of reprocess config for now
storage = QLStorageSource(config)
path = storage.plate_path(plate)
factory = ExperimentMetadataObjectFactory()
qlp = factory.parse_plate(path)
c.wells = qlp.analyzed_wells
c.original_source = plate.name
c.plate_template_id = None
c.plate_setup_id = None
c.id = id
return self.__display(rowcol_order=qlp.acquisition_order)
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
def command(self):
app = self.load_wsgi_app()
storage = QLStorageSource(app.config)
# enforce config.ini
if len(self.args) > 1:
plate_id = int(self.args[0])
else:
plate_id = 1 ## default start....
plate_metrics = Session.query(PlateMetric).filter(PlateMetric.plate_id >= plate_id)\
.options(joinedload(PlateMetric.plate, innerjoin=True))\
.options(joinedload(PlateMetric.reprocess_config))
# TODO come up with version that takes care of reprocessed plates as well
# (by iterating through analysis groups, most likely)
for pm in plate_metrics:
if pm.from_reprocessed:
continue
plate = dbplate_tree(pm.plate_id)
try:
plate_path = storage.plate_path(plate)
except Exception:
print "Could not read plate: %s" % pm.plate_id
continue
try:
qlplate = get_plate(plate_path)
except Exception:
print "Could not read plate: %s" % plate_path
continue
if not qlplate:
print "Could not read plate: %s" % plate_path
continue
else:
print "Processing %s: %s..." % (pm.plate_id, plate_path)
self.process_plate(qlplate, pm)
def command(self):
app = self.load_wsgi_app()
# enforce config.ini
if len(self.args) < 2:
raise ValueError, self.__class__.usage
analysis_group_id = int(self.args[0])
if len(self.args) == 3:
reprocess_config = Session.query(ReprocessConfig).filter_by(code=self.args[1]).one()
reprocess_config_id = reprocess_config.id
else:
reprocess_config = None
reprocess_config_id = None
analysis_group = Session.query(AnalysisGroup).get(analysis_group_id)
if not analysis_group:
raise ValueError, "No analysis group for id %s" % analysis_group_id
plates = analysis_group.plates
# todo: add in reprocess config id
for plate in plates:
pm = [pm for pm in plate.metrics if pm.reprocess_config_id == reprocess_config_id]
# should only be of length 1, but just to be safe
for p in pm:
Session.delete(p)
# TODO: how to make this whole operation transactional
Session.commit()
# this is a little tricky in the ORM world. only get the
# ids of the analysis_group plates, so that you can load the plate
# and all the necessary children
plate_ids = [plate.id for plate in plates]
if reprocess_config_id is None:
storage = QLStorageSource(app.config)
for id in plate_ids:
dbplate = dbplate_tree(id)
plate_path = storage.plate_path(dbplate)
print "Reading/updating metrics for %s" % plate_path
qlplate = get_plate(plate_path)
if not qlplate:
print "Could not read plate: %s" % plate_path
continue
plate_metrics = get_beta_plate_metrics(dbplate, qlplate)
Session.add(plate_metrics)
del qlplate
else:
data_root = app.config['qlb.reprocess_root']
file_source = QLPReprocessedFileSource(data_root, reprocess_config)
for id in plate_ids:
dbplate = dbplate_tree(id)
# TODO: right abstraction?
plate_path = file_source.full_path(analysis_group, dbplate)
print "Reading/updating metrics for %s" % plate_path
qlplate = get_plate(plate_path)
if not qlplate:
print "Could not read plate: %s" % plate_path
continue
plate_metrics = get_beta_plate_metrics(dbplate, qlplate, reprocess_config)
Session.add(plate_metrics)
del qlplate
Session.commit()