class Chunklist(db.Model):
__tablename__ = 'chunklist'
id = db.Column(db.Integer, primary_key=True)
filename = db.Column(db.String(100))
date = db.Column(db.DateTime())
end_time = db.Column(db.DateTime())
chunks = db.relationship('Chunk', backref='chunklist', lazy='dynamic')
user_id = db.Column(db.Integer, db.ForeignKey('user.id'))
case = db.relationship('Case', backref='chunklist', uselist=False)
def __init__(self, filename='', date='', user_id=''):
self.filename = filename
self.date = date.replace(microsecond=0)
self.user_id = user_id
def set_done(self, case):
self.case = case
self.end_time = datetime.datetime.now().replace(microsecond=0)
@property
def validation_filename(self):
return '_'.join(self.filename.split('_')[:3])
@property
def duration(self):
if self.end_time:
return str(self.end_time - self.date)
else:
return "Not done"
def __repr__(self):
return self.filename
class Region(db.Model):
__tablename__ = 'region'
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(50))
code = db.Column(db.String(10))
cases = db.relationship('Case', backref='region', lazy='dynamic')
provinces = db.relationship('Province', backref='region', lazy='dynamic')
def __init__(self, name='', code=''):
self.name = name
self.code = code
def __repr__(self):
return self.name
class Infection(db.Model):
__tablename__ = 'infection'
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(80))
specimen_type = db.Column(db.String(80))
diagnoses = db.relationship('ParType', backref='infection', lazy='dynamic')
cases = db.relationship('Case', backref='infection', lazy='dynamic')
def __init__(self, name, specimen_type):
self.name = name
self.specimen_type = specimen_type
def __repr__(self):
return self.name
class UserType(db.Model):
__tablename__ = 'usertype'
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(80), unique=True)
users = db.relationship('User', backref='usertype', lazy='dynamic')
@staticmethod
def get_administrator():
return UserType.query.filter(UserType.name=='Administrator').first()
@staticmethod
def get_microscopist():
return UserType.query.filter(UserType.name=='Medical Technologist').first()
@staticmethod
def get_doctor():
return UserType.query.filter(UserType.name=='Validator').first()
@staticmethod
def get_labeler():
return UserType.query.filter(UserType.name=='Labeler').first()
@staticmethod
def get_localadmin():
return UserType.query.filter(UserType.name=='Local Administrator').first()
def __init__(self, name=""):
self.name = name
def __repr__(self):
return '<UserType %r>' % self.name
def __str__(self):
return self.name
class Province(db.Model):
__tablename__ = 'province'
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String(50))
code = db.Column(db.String(10))
cases = db.relationship('Case', backref='province', lazy='dynamic')
municipalities = db.relationship('Municipality', backref='province', lazy='dynamic')
region_id = db.Column(db.Integer, db.ForeignKey('region.id'))
def __init__(self, name='', code=''):
self.name = name
self.code = code
def __repr__(self):
return self.name
@property
def serialize(self):
return {'id': self.id, 'name': self.name}
class Image(db.Model):
__tablename__ = 'image'
id = db.Column(db.Integer, primary_key=True)
case_id = db.Column(db.Integer, db.ForeignKey('case.id'))
im = db.Column(db.BLOB)
number = db.Column(db.Integer)
patches = db.relationship('Patch', backref='image', lazy='dynamic')
# images are labeled/tagged by several labelers
# is_tagged = db.Column(db.Boolean, default=False)
'''
def __init__(self, path="", case=""):
with open(path, 'r') as f:
self.im = f.read()
self.case = case
'''
def create_image(self, path="", case=""):
with open(path, 'rb') as f:
self.im = f.read()
self.case = case
class ParType(db.Model):
__tablename__ = 'partype'
id = db.Column(db.Integer, primary_key=True)
infection_id = db.Column(db.Integer, db.ForeignKey('infection.id'))
name = db.Column(db.String(80))
negative = db.Column(db.Boolean())
patches = db.relationship('Patch', backref='partype', lazy='dynamic')
def __init__(self, name="", infection="", negative=0):
self.name = name
self.infection = infection
self.negative = negative
@property
def type(self):
return self.name
def __repr__(self):
return self.name
def __str__(self):
return self.name
class User(db.Model, UserMixin):
__tablename__ = 'user'
id = db.Column(db.Integer, primary_key=True)
username = db.Column(db.String(80), unique=True)
password = db.Column(db.String(120))
firstname = db.Column(db.String(100))
lastname = db.Column(db.String(100))
usertype_id = db.Column(db.Integer, db.ForeignKey('usertype.id'))
case = db.relationship('Case', backref='user', lazy='dynamic')
contact = db.Column(db.String(80))
email = db.Column(db.String(80), unique=True)
chunklists = db.relationship('Chunklist', backref='user', lazy='dynamic')
validations = db.relationship('Validation', backref='user', lazy='dynamic')
test = db.Column(db.Boolean)
"""
@models_committed.connect_via(app)
def on_models_committed(sender, changes):
for obj, method in changes:
if method == 'insert' and type(obj) == User:
body = '''Greetings, %s %s! You have successfully been registered to the system. Your temporary password is <b>%s</b>.<br><br>Below are your account details:<br><br>Username: %s<br>User type: %s<br>Contact number: %s<br>Email: %s<br><br>Please login and change your password. Thank you!''' % (obj.firstname, obj.lastname, '123', obj.username, obj.usertype, obj.contact, obj.email)
msg = Message('Outbreak Monitoring', sender="*****@*****.**", recipients=['*****@*****.**',obj.email])
msg.html = body
mail.send(msg)
"""
@validates('password')
def update_password(self, key, value):
Database.query.first().modified = datetime.datetime.now()
return value
@staticmethod
def hash_password(password):
return hashlib.sha1(password).hexdigest()
def is_administrator(self):
return self.usertype == UserType.get_administrator()
def is_microscopist(self):
return self.usertype == UserType.get_microscopist()
def is_doctor(self):
return self.usertype == UserType.get_doctor()
def is_labeler(self):
return self.usertype == UserType.get_labeler()
def is_localadmin(self):
return self.usertype == UserType.get_localadmin()
def __init__(self, firstname="", lastname="", username="", password="", contact="", email=""):
self.firstname = firstname
self.lastname = lastname
self.username = username
self.password = password
self.contact = contact
self.email = email
def __repr__(self):
return '<User %r %r (%r)>' % (self.firstname, self.lastname, self.username)
def __str__(self):
return self.username
class Case(db.Model):
__tablename__ = 'case'
id = db.Column(db.Integer, primary_key=True)
date = db.Column(db.DateTime())
# parasite = db.Column(db.String(100))
description = db.Column(db.String(1000))
comment = db.Column(db.String(1000))
lat = db.Column(db.Float)
lng = db.Column(db.Float)
user_id = db.Column(db.Integer, db.ForeignKey('user.id'))
images = db.relationship('Image', backref='case', lazy='dynamic')
test = db.Column(db.Boolean)
# partype_id = db.Column(db.Integer, db.ForeignKey('partype.id'))
infection_id = db.Column(db.Integer, db.ForeignKey('infection.id'))
region_id = db.Column(db.Integer, db.ForeignKey('region.id'))
province_id = db.Column(db.Integer, db.ForeignKey('province.id'))
municipality_id = db.Column(db.Integer, db.ForeignKey('municipality.id'))
chunklist_id = db.Column(db.Integer, db.ForeignKey('chunklist.id'))
parasite_validator = db.Column(db.String(100))
description_validator = db.Column(db.String(1000))
patient_id = db.Column(db.String(100))
validations = db.relationship('Validation', backref='case', lazy='dynamic')
# def __init__(self, date="", partype="", description="", lat="", lng="", test="", region="", province="", municipality="", patient_id=""):
def __init__(self, date="", description="", lat="", lng="", test="", region="", province="", municipality="", infection=""):
self.date = date
self.description = description
self.lat = lat
self.lng = lng
self.test = test
if region == '':
self.region = None
else:
self.region = region
if province == '':
self.province = None
else:
self.province = province
if municipality == '':
self.municipality = None
else:
self.municipality = municipality
if infection == '':
self.infection = None
else:
self.infection = infection
# if partype == '':
# self.partype = None
# else:
# self.partype = partype
# if patient_id == '':
# self.patient_id = None
# else:
# self.patient_id = patient_id
def __repr__(self):
return '<Case %r>' % self.id
def __str__(self):
return str(self.id)
@property
def code(self):
return "%s-%s-%s" % (self.region.code, self.province.code, self.id)
@property
def duration(self):
if self.chunklist:
return self.chunklist.duration
else:
return 'Not recorded'
@property
def final_validation(self):
return Validation.query.filter(Validation.final==True, Validation.case==self).first()
@property
def finalized(self):
return self.final_validation != None
@property
def finalized_text(self):
return "Done" if self.finalized else "Pending"
@property
def validator(self):
validation = self.final_validation
if validation:
return validation.user
return None
@property
def validator_contacts(self):
validator = self.validator
if validator:
return "%s / %s" % (validator.contact, validator.email)
return None