class ProjectMemship(db.Model):
user_email = db.Column(db.String(120),
db.ForeignKey('user.email'),
primary_key=True)
project_id = db.Column(db.Integer,
db.ForeignKey('project.id'),
primary_key=True)
is_project_admin = db.Column(db.Boolean, nullable=False)
def __repr__(self):
return "<ProjectMemship - User: {} - Project: {}>".format(
self.user_email, self.project_id)
class MarkerAllele(db.Model):
marker = db.Column(db.String(15),
db.ForeignKey('marker.id'),
primary_key=True)
allele = db.Column(db.String(1), primary_key=True)
def __repr__(self):
return "<MarkerAllele - Marker: {} - Allele: {}>".format(
self.marker, self.allele)
class Genotype(db.Model):
id = db.Column(db.Integer, primary_key=True)
ind_id = db.Column(db.Integer,
db.ForeignKey('individual.id'),
nullable=False)
marker = db.Column(db.String(20),
db.ForeignKey('marker.id'),
nullable=False)
call_1 = db.Column(db.String(1), nullable=False)
call_2 = db.Column(db.String(2), nullable=False)
__table_args__ = (UniqueConstraint('ind_id', 'marker',
name="_geno_uc"), {})
def __repr__(self):
return "<Genotype - ID: {}>".format(self.id)
@staticmethod
def query_by_project(proj_id):
subquery = db.session.query(
Individual.id).filter_by(project_id=proj_id)
return Genotype.query.filter(Genotype.ind_id.in_(subquery))
class Phenotype(db.Model):
id = db.Column(db.Integer, primary_key=True)
ind_id = db.Column(db.Integer,
db.ForeignKey('individual.id'),
nullable=False)
name = db.Column(db.String(30), nullable=False)
value = db.Column(db.String(50), nullable=False)
__table_args__ = (UniqueConstraint('ind_id', 'name', name="_pheno_uc"), {})
def __repr__(self):
return "<Phenotype - ID: {}>".format(self.id)
@staticmethod
def query_by_project(proj_id):
subquery = db.session.query(
Individual.id).filter_by(project_id=proj_id)
return Phenotype.query.filter(Phenotype.ind_id.in_(subquery))
class Individual(db.Model):
id = db.Column(db.Integer, primary_key=True)
project_id = db.Column(db.Integer,
db.ForeignKey('project.id'),
nullable=False)
clinic_id = db.Column(db.String(5), nullable=False)
family_id = db.Column(db.String(15), nullable=False)
member_id = db.Column(db.Integer, nullable=False)
gender = db.Column(db.Integer, nullable=False)
__table_args__ = (UniqueConstraint('project_id',
'clinic_id',
'family_id',
'member_id',
name="_individual_uc"), {})
def __repr__(self):
return "<Individual - ID: {}>".format(self.id)
def get_full_id(self):
return self.clinic_id + "_" + self.family_id + "_" + self.member_id