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 update_reprocess_analysis_group_data(analysis_group, reprocess_config, config, logger):
"""
Given an analysis_gropu and repocessor, relaod each into qtools
"""
update_status = 0
plates = analysis_group.plates
# remove old metrics if present
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()
plate_ids = [plate.id for plate in plates]
data_root = 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()
return update_status
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()
