def setup(session):
""" populate database with essential GenAF data, mostly taken from FATools constants """
EK.bulk_insert(ek_initlist, dbsession=session)
# get default group, which is system
adm_group = Group.search("_DataAdm_", dbsession=session)
# create undefined marker
marker = Marker(code="undefined", species="X")
cerr("INFO - marker 'undefined' created.")
session.add(marker)
# create ladder marker
marker = Marker(code="ladder", species="X")
cerr("INFO - marker 'ladder' created.")
session.add(marker)
# create combined marker
marker = Marker(code="combined", species="X")
cerr("INFO - marker 'combined' created.")
session.add(marker)
# create default panel
panel = Panel(code="undefined", group_id=adm_group.id)
cerr("INFO - panel 'undefined' created.")
session.add(panel)
# create default batch
batch = Batch(code="default", group_id=adm_group.id, assay_provider_id=adm_group.id, species="X")
cerr("INFO - default batch created.")
session.add(batch)
def update(self, obj):
self._update(obj)
session = object_session(self) or self._dbh_session_
if type(obj) == dict:
if 'group' in obj:
with session.no_autoflush:
group = Group.search(obj['group'], session)
self.group = group
else:
raise NotImplementedError()
# verify that each marker in data exists
session = object_session(self) or self._dbh_session_
for m_code in self.data['markers']:
m = Marker.search(m_code, session)
if m is None:
cerr("ERR: can't find marker: %s" % m_code)
sys.exit(1)
