def upgrade(migrate_engine):
meta = sqlalchemy.MetaData()
meta.bind = migrate_engine
base_transfer_action = sqlalchemy.Table('base_transfer_action',
meta,
autoload=True)
base_transfer_action.c.info.alter(type=types.Binary(4294967295))
def get_columns(self, engine, table_name, schema=None, **kw):
cols = engine.connect().connection.get_columns(table_name)
get_coldef = lambda x, y: {
"name": x,
"type": BQDialect.__TYPE_MAPPINGS.get(y, types.Binary()),
"nullable": True,
"default": None
}
return [get_coldef(*col) for col in cols]
class IP(types.TypeDecorator):
"""Implements an IP as an integer."""
impl = types.Binary(length=16)
def __init__(self):
pass
def process_bind_param(self, value, engine):
try:
return inet.pton(value);
except:
l = len (value)
if l == 4: return inet.IPV4PREFIX + value
if l == 16: return value
raise Exception ('Invalid IP:(' + value +')')
def process_result_value(self, value, engine):
return inet.ntop(value);
def is_mutable(self):
return False
def test_should_unknown_sqlalchemy_field_raise_exception():
re_err = "Don't know how to convert the SQLAlchemy field"
with pytest.raises(Exception, match=re_err):
get_field(types.Binary())
class Assay(Base, AssayMixIn):
__tablename__ = 'assays'
id = Column(types.Integer, primary_key=True)
filename = Column(types.String(128), nullable=False, index=True)
runtime = Column(types.DateTime, nullable=False)
rss = Column(types.Float, nullable=False, default=-1)
dp = Column(types.Float, nullable=False, default=-1)
score = Column(types.Float, nullable=False, default=-1)
z = deferred(Column(NPArray))
ladder_peaks = Column(types.Integer, nullable=False, default=-1)
size_standard = Column(types.String(32), nullable=False, default='')
sample_id = Column(types.Integer,
ForeignKey('samples.id', ondelete='CASCADE'),
nullable=False)
sample = relationship(Sample,
uselist=False,
backref=backref('assays', lazy='dynamic'))
panel_id = Column(types.Integer, ForeignKey('panels.id'), nullable=False)
panel = relationship(Panel, uselist=False)
ladder_id = Column(types.Integer,
ForeignKey('channels.id',
use_alter=True,
name='ladderchannel_fk'),
nullable=True)
#channels = relationship('Channel', primaryjoin = "Assay.id == Channel.id", lazy='dynamic',
# post_update = True,
# backref = backref('assay', uselist=False))
ladder = relationship('Channel',
uselist=False,
primaryjoin="Assay.ladder_id == Channel.id")
status = Column(types.String(32), nullable=False)
method = deferred(Column(types.String(16), nullable=False))
report = deferred(Column(types.String(512), nullable=False, default=''))
remark = deferred(Column(types.String(1024), nullable=False, default=''))
exclude = deferred(Column(types.String(128), nullable=False, default=''))
raw_data = deferred(Column(types.Binary(), nullable=False))
""" raw data for this assay (FSA file content) """
__table_args__ = (UniqueConstraint('filename', 'panel_id', 'sample_id'), )
def new_channel(self,
raw_data,
data,
dye,
wavelen,
status,
median,
mean,
max_height,
min_height,
std_dev,
initial_marker=None,
initial_panel=None):
""" create new channel and added to this assay """
if not initial_marker:
initial_marker = Marker.search('undefined',
session=object_session(self))
if not initial_panel:
initial_panel = Panel.search('undefined',
session=object_session(self))
channel = Channel(raw_data=data,
data=data,
dye=dye,
wavelen=wavelen,
status=status,
median=median,
mean=mean,
max_height=max_height,
min_height=min_height,
std_dev=std_dev)
channel.assay = self
channel.marker = initial_marker
channel.panel = initial_panel
return channel
def get_ladder(self):
""" get ladder channel """
assert self.ladder_id, "ERR/PROG - pls make sure ladder_id is not null!"
session = object_session(self)
return Channel.get(self.ladder_id, session)
sm = sessionmaker(autoflush=True,
bind=engine,
expire_on_commit=False,
extension=ZopeTransactionExtension())
meta.engine = engine
meta.Session = scoped_session(sm)
users_table = Table("users", metadata,
Column('id', types.Integer, primary_key=True),
Column('username', types.Unicode(50)),
# ElGamal user's public key.
Column('pubkey', types.Text),
# Used in the login/authenticate challenge
Column('logging_token', types.Binary(35)),
# Time until the token is valid.
Column('logging_timeout', types.DateTime),
# This stamp is used to wipe users which haven't 'setup'
# their account before this date/time
Column('waiting_setup', types.DateTime, nullable=True),
Column('created_time', types.DateTime,
default=datetime.now),
# Admin flag, allows to add users, and grant access.
Column('is_admin', types.Boolean, default=False)
)
usergroups_table = Table('users_groups', metadata,
Column('id', types.Integer, primary_key=True),
Column('user_id', types.Integer,
ForeignKey('users.id')),
person = schema.Table(
'person', meta.metadata,
schema.Column('id',
types.Integer,
schema.ForeignKey('node.id'),
primary_key=True),
schema.Column('user_id',
types.Integer,
schema.ForeignKey('user.id'),
nullable=True),
schema.Column('event_id',
types.Integer,
schema.ForeignKey('event.id'),
nullable=False),
schema.Column('fullname', types.Unicode(50), nullable=False),
schema.Column('avatar', types.Binary()),
schema.Column('details', types.Unicode(500)),
schema.Column('created', types.DateTime(), default=datetime.now()),
schema.Column('updated', types.DateTime(), onupdate=datetime.now()))
article = schema.Table(
'article', meta.metadata,
schema.Column('id',
types.Integer,
schema.ForeignKey('node.id'),
primary_key=True),
schema.Column('title', types.Unicode(50), nullable=False),
schema.Column('path', types.Unicode(), nullable=False, unique=True),
schema.Column('label', types.Unicode(50)),
schema.Column('content', types.Unicode(), nullable=False),
schema.Column('published', types.DateTime),