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 setup_db( *ops ):
""" setup the database (create tables, etc) and populate with basic data """
base = get_base()
# WARN: use alembic to create initial tables
#base.metadata.create_all()
with transaction.manager:
if get_datalogger():
get_clsreg().sync()
with transaction.manager:
EK.bulk_insert( ek_initlist )
Group.bulk_insert( essential_groups )
file = File( path='/', type='file/folder', mimetype='application/x-directory',
group_id = Group._id('_SysAdm_'), permanent = True )
dbsession.add( file )
for op in ops:
op()
def setup(dbsession):
assert dbsession
EK.bulk_insert( ek_initlist, dbsession=dbsession)
