def do_importgroup(args, dbh, settings):
cerr('Importing group')
groups = yaml.load(open(args.importgroup))
from rhombus.models.user import UserClass, Group
Group.bulk_insert(groups, dbsession=dbh.session())
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( dbh ):
""" populate the database with basic, essential data """
if get_datalogger():
get_clsreg().sync()
session.commit()
dbsession = dbh.session()
EK.bulk_update( ek_initlist, dbsession=dbsession )
Group.bulk_insert( essential_groups, dbsession=dbsession )
UserClass.bulk_insert( system_userclass, dbsession=dbsession )
group_id = Group._id('_SysAdm_', dbsession)
file = File( path='/', group_id = group_id, permanent = True )
dbsession.add( file )
file.type = 'file/folder'
file.mimetype = 'application/x-directory'
cerr('INFO: root password is %s\n' % root_password)
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 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)
def index(request):
""" list groups """
dbh = get_dbhandler()
groups = Group.query(dbh.session())
html, code = format_grouptable(groups, request)
if request.user.has_roles(SYSADM):
add_button = ( 'New group',
request.route_url('rhombus.group-edit', id=0)
)
bar = selection_bar('group-ids', action=request.route_url('rhombus.group-action'),
add = add_button)
html, code = bar.render(html, code)
return render_to_response('rhombus:templates/group/index.mako',
{ 'html': html,
'code': code,
}, request=request )
def populate_db( dbsession, initial_groups=None, initial_userclass=None ):
if initial_groups:
Group.bulk_insert( initial_groups, dbsession=dbsession )
if initial_userclass:
UserClass.bulk_insert( initial_userclass, dbsession=dbsession )