class BioObject(db.Model):
__tablename__ = "bioobject" # Add table name to be None
__mapper_args__ = {
'polymorphic_identity': 'bioobject',
'polymorphic_on': 'type',
}
object_collection_id = db.Column(db.Integer,
db.ForeignKey('bioobjectcollection.id'))
collection = db.relationship(BioObjectCollection)
type = db.Column(db.String(32))
class Synapse(BioObject):
__tablename__ = None # Add table name to be None
__mapper_args__ = {'polymorphic_identity': 'synapse'}
oid = db.Column(db.String(50))
areas = db.Column(
Geometry(geometry_type="MULTIPOLYGONZ",
management=True,
use_typmod=False,
srid=SYNAPSE_SRID,
dimension=3))
class SourceChannel(NamedModel, db.Model):
__tablename__ = 'sourcechannel'
volume_id = db.Column(db.Integer, db.ForeignKey('volume.id'))
source_url = db.Column(db.String(250), nullable=False)
default_channel = db.Column(db.Boolean, nullable=False, default=False)
type = db.Column(db.String(32), default='image')
__mapper_args__ = {
'polymorphic_on': 'type',
'polymorphic_identity': ''
}
class Link(NamedModel, db.Model):
__tablename__ = 'link'
type = db.Column(db.String(32))
link = db.Column(db.String(10000))
__mapper_args__ = {
'polymorphic_on': 'type',
'polymorphic_identity': 'link'
}
def get_link_html(self):
return '<a href="{}">{}</a>'.format(self.link, self.name)
class BioObjectCollection(NamedModel, db.Model):
__tablename__ = 'bioobjectcollection'
volume_id = db.Column(db.Integer, db.ForeignKey('volume.id'))
volume = db.relationship('Volume')
link_id = db.Column(db.Integer, db.ForeignKey('link.id'))
link = db.relationship('Link')
objects = db.relationship('BioObject')
type = db.Column(db.String(32))
__mapper_args__ = {
'polymorphic_on': 'type',
'polymorphic_identity': 'employee'
}
class RatingSource(NamedModel, db.Model):
__tablename__ = "ratingsource"
type = db.Column(db.String(32))
__mapper_args__ = {
'polymorphic_identity': 'ratingsource',
'polymorphic_on': 'type',
}
class Rating(TimestampMixin, db.Model):
__tablename__ = "rating"
type = db.Column(db.String(32))
object_id = db.Column(
db.Integer,
db.ForeignKey('bioobject.id'),
nullable=False,
)
rating_source_id = db.Column(
db.Integer,
db.ForeignKey('ratingsource.id'),
nullable=False,
)
classificationtype_id = db.Column(db.Integer,
db.ForeignKey('classificationtype.id'),
nullable=False)
confidence = db.Column(db.Float)
classificationtype = db.relationship('ClassificationType')
rating_source = db.relationship('RatingSource')
object = db.relationship('BioObject')
bool_rating = db.Column(db.Boolean)
tert_rating = db.Column(db.Integer)
def get_rating(self):
'''generic function, need to implement for class'''
pass
__mapper_args__ = {
'polymorphic_identity': 'rating',
'polymorphic_on': 'type',
}
class Volume(NamedModel, db.Model):
channels = db.relationship('SourceChannel', backref='volume')
dataset_id = db.Column(db.Integer, db.ForeignKey('data_set.id'))
dataset = db.relationship('DataSet')
links = db.relationship('VolumeLink', backref='volume')
synapse_collections = db.relationship('SynapseCollection',
backref='synvolume')
def get_neuroglancer_layers(self):
ds = []
for chan in self.channels:
if chan.default_channel:
d = {
'source': chan.source_url,
'blend': 'additive'
}
if chan.default_color:
d['color'] = chan.default_color
ds.append(d)
return ds
class NamedModel(object):
name = db.Column(db.String(100), nullable=False)
def __repr__(self):
return "{}({})".format(self.name, self.id)
class MachineLearningSource(RatingSource):
algorithm = db.Column(db.String(100))
__tablename__ = None
__mapper_args__ = {
'polymorphic_identity': 'machinelearning',
}
class UserRatingSource(RatingSource):
user_id = db.Column(db.Integer)
__tablename__ = None
__mapper_args__ = {
'polymorphic_identity': 'user',
}
class SynapseCollection(BioObjectCollection):
__tablename__ = None # Add table name to be None
__mapper_args__ = {'polymorphic_identity': 'synapsecollection'}
synapse_collection_type = db.Column(db.String(100))
class ClassificationType(NamedModel, db.Model):
__tablename__ = "classificationtype"
rating_type = db.Column(db.String(40))
class VolumeLink(Link):
__tablename__ = None
volume_id = db.Column(db.Integer, db.ForeignKey('volume.id'))
__mapper_args__ = {
'polymorphic_identity': 'volumelink'
}
class TimestampMixin(object):
created = db.Column(db.DateTime, nullable=False, default=datetime.now())
updated = db.Column(db.DateTime, onupdate=datetime.now())
class ImageChannel(SourceChannel):
__tablename__ = None
default_color = db.Column(db.String(1))
__mapper_args__ = {
'polymorphic_identity': 'image'
}
class ConsensusSource(RatingSource):
rating_sources = db.Column(ARRAY(db.Integer))
__tablename__ = None
__mapper_args__ = {
'polymorphic_identity': 'consensus',
}
class DataSet(NamedModel, db.Model):
render_project = db.Column(db.String(50))
render_owner = db.Column(db.String(50))
volumes = db.relationship('Volume', backref='data_set')