class Marker(db.Model):
id = db.Column(db.String(15), primary_key=True)
chromosome = db.Column(db.Integer, nullable=False)
position = db.Column(db.Integer, nullable=False)
def __repr__(self):
return "<Marker - ID: {}>".format(self.id)
class User(UserMixin, db.Model):
email = db.Column(db.String(120), primary_key=True)
full_name = db.Column(db.String(120), nullable=False)
password_hash = db.Column(db.String(250), nullable=False)
is_sys_admin = db.Column(db.Boolean, nullable=False)
memships = db.relationship('ProjectMemship',
backref='user',
lazy='dynamic')
def __repr__(self):
return '<User {} - {}>'.format(self.email, self.full_name)
def __str__(self):
return self.full_name + " - " + self.email
def get_id(self):
return self.email
def set_password(self, password):
self.password_hash = generate_password_hash(
password,
method=app.config['HASH_METHOD'],
salt_length=app.config['SALT_LENGTH'])
def check_password(self, password):
return check_password_hash(self.password_hash, password)
def get_projects(self):
projects = []
for memship in self.memships:
projects.append(memship.project)
return projects
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 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 SystemLog(db.Model):
id = db.Column(db.Integer, primary_key=True)
time = db.Column(db.DateTime, default=datetime.utcnow)
message = db.Column(db.String(150), nullable=False)
user_ip = db.Column(db.String(15), nullable=False)
# User email not stored as foreign key so that logs will persist
# after users are deleted
user_email = db.Column(db.String(120), nullable=False)
def __init__(self, user_ip, user_email, message):
self.message = message
self.user_ip = user_ip
self.user_email = user_email
def __repr__(self):
return "<SystemLog - ID: {}>".format(self.id)
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 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 Project(db.Model):
id = db.Column(db.Integer, primary_key=True)
title = db.Column(db.String(100), nullable=False)
desc = db.Column(db.String(300), nullable=False)
memships = db.relationship('ProjectMemship',
backref='project',
lazy='dynamic',
cascade="all, delete-orphan")
def __repr__(self):
return '<Project {}>'.format(self.id)
def __str__(self):
return str(self.id) + " : " + self.title
def get_members(self):
# Each element is a tuple of the user object and whether they are a project admin
members = []
for memship in self.memships:
memship.user.is_project_admin = memship.is_project_admin
members.append(memship.user)
return members
class ProjectLog(db.Model):
id = db.Column(db.Integer, primary_key=True)
time = db.Column(db.DateTime, default=datetime.utcnow)
message = db.Column(db.String(150), nullable=False)
user_ip = db.Column(db.String(15), nullable=False)
# User email and project id not stored as foreign keys so that
# logs will persist after users and projects are deleted
user_email = db.Column(db.String(120), nullable=False)
project_id = db.Column(db.Integer, nullable=False)
def __init__(self, project_id, user_ip, user_email, message):
self.project_id = project_id
self.message = message
self.user_ip = user_ip
self.user_email = user_email
def __repr__(self):
return "<ProjectLog - ID: {}".format(self.id)
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