/
populator.py
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/
populator.py
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import datetime
import os
from random import randint, random, choice
from sqlalchemy_imageattach.entity import Image, image_attachment
from sqlalchemy_imageattach.context import store_context
from database_setup import Base, User, Antibody, Cytotoxin, Adc
from database_setup import AntibodyLot, CytotoxinLot, AdcLot
from database_setup import UserImg, AntibodyImg, CytotoxinImg, AdcImg
from helper import attach_picture, attach_picture_url
from init_db import session
from settings import app_path, fs_store
def create_random_date():
today = datetime.date.today()
difference = randint(0, 720)
lotdate = today - datetime.timedelta(days=difference)
return lotdate
# Add dummy user
def create_user(name, email, picture):
user = User(name=name, email=email)
session.add(user)
session.commit()
new_user_id = session.query(User).filter_by(email=email).one().id
if picture.startswith("https"):
attach_picture_url(User, new_user_id, picture)
else:
attach_picture(User, new_user_id, picture)
# Add Antibody
def create_antibody():
antibody1 = Antibody(name='Amatuximab', weight=144330,
target='Mesothelin', user_id=1)
session.add(antibody1)
session.commit()
antibody2 = Antibody(name='Brentuximab', weight=153000,
target='CD30', user_id=2)
session.add(antibody2)
session.commit()
antibody3 = Antibody(name='Gemtuzumab', weight=152000,
target='CD33', user_id=3)
session.add(antibody3)
session.commit()
antibody4 = Antibody(name='Trastuzumab', weight=148000,
target='HER2/neu', user_id=1)
session.add(antibody4)
session.commit()
antibody5 = Antibody(name='Vorsetuzumab', weight=150000,
target='CD70', user_id=2)
session.add(antibody5)
session.commit()
# Add Antibody Lot
def create_antibody_lot():
for x in range(20):
antibody_lot = AntibodyLot(
date=create_random_date(),
aggregate=randint(0, 5)+round(random(), 2),
endotoxin=randint(0, 10)+round(random(), 2),
concentration=randint(0, 10)+round(random(), 2),
vial_volume=choice([1, 0.2, 0.5]),
vial_number=randint(1, 100),
antibody_id=randint(1, 5),
user_id=randint(1, 3))
session.add(antibody_lot)
session.commit()
def create_cytotoxin():
cytotoxin1 = Cytotoxin(name='Maytansine',
weight=692.19614,
drug_class='tubulin inhibitor',
user_id=1)
cytotoxin2 = Cytotoxin(name='Monomethyl auristatin E',
weight=717.97858,
drug_class='antineoplastic agent',
user_id=2)
cytotoxin3 = Cytotoxin(name='Calicheamicin',
weight=1368.34,
drug_class='enediyne antitumor antibotics',
user_id=3)
cytotoxin4 = Cytotoxin(name='Mertansine',
weight=477.47,
drug_class='tubulin inhibitor',
user_id=1)
cytotoxin5 = Cytotoxin(name='Pyrrolobenzodiazepine',
weight=25827,
drug_class='DNA crosslinking agent',
user_id=2)
session.add_all([cytotoxin1, cytotoxin2, cytotoxin3,
cytotoxin4, cytotoxin5])
session.commit()
def create_cytotoxin_lot():
for x in range(20):
cytotoxin_lot = CytotoxinLot(date=create_random_date(),
purity=randint(80, 99)+round(random(), 2),
concentration=randint(0, 10)+round(random(), 2),
vial_volume=choice([1, 0.2, 0.5]),
vial_number=randint(1, 100),
cytotoxin_id=randint(1, 5),
user_id=randint(1, 3))
session.add(cytotoxin_lot)
session.commit()
def antibody_lot():
total = []
for x in range(1, 6):
lotlist = []
antibodies = (session.query(AntibodyLot)
.filter(AntibodyLot.antibody_id == x).all())
for antibody in antibodies:
lotlist.append(antibody.id)
total.append(lotlist)
return total
def cytotoxin_lot():
total = []
for x in range(1, 6):
lotlist = []
cytotoxins = (session.query(CytotoxinLot)
.filter(CytotoxinLot.cytotoxin_id == x).all())
for cytotoxin in cytotoxins:
lotlist.append(cytotoxin.id)
total.append(lotlist)
return total
def create_adc():
adc1 = Adc(name='Amatuximab maytansine',
chemistry='lysine conjugation',
user_id=1)
adc2 = Adc(name='Brentuximab vedotin',
chemistry='cysteine conjugation',
user_id=2)
adc3 = Adc(name='Gemtuzumab ozogamicin',
chemistry='site-specific conjugation',
user_id=3)
adc4 = Adc(name='Trastuzumab emtansine',
chemistry='engineered cysteine conjugation',
user_id=1)
adc5 = Adc(name='Vorsetuzumab pyrrolobenzodiazepine',
chemistry='enzyme-assisted conjugation',
user_id=2)
session.add_all([adc1, adc2, adc3, adc4, adc5])
session.commit()
def create_adc_lot():
lot = [1, 2, 3, 4, 5]
for x in range(20):
error = True
while error:
randomlot = choice(lot)
try:
id1 = choice(antibody_lot()[randomlot-1])
id2 = choice(cytotoxin_lot()[randomlot-1])
except IndexError:
lot.remove(randomlot)
else:
error = False
adclot = AdcLot(date=create_random_date(),
aggregate=randint(0, 5)+round(random(), 2),
endotoxin=randint(0, 10)+round(random(), 2),
concentration=randint(0, 10)+round(random(), 2),
vial_volume=choice([1, 0.2, 0.5]),
vial_number=randint(1, 100),
adc_id=randomlot,
antibodylot_id=id1,
cytotoxinlot_id=id2,
user_id=randint(1, 3))
session.add(adclot)
session.commit()
if __name__ == '__main__':
create_user('Wiseley Wu', 'wiseleywu@gmail.com', 'https://lh6.googleusercontent.com/-45KCJFuShPk/AAAAAAAAAAI/AAAAAAAArRw/E7__AYvGSOQ/photo.jpg')
create_user('John Doe',
'john.doe@gmail.com',
os.path.join(app_path, 'static/images/user.png'))
create_user('Jane Doe',
'jane.doe@gmail.com',
os.path.join(app_path, 'static/images/user.png'))
create_antibody()
create_antibody_lot()
create_cytotoxin()
create_cytotoxin_lot()
create_adc()
create_adc_lot()
for x in range(1, 6):
attach_picture(Antibody,
x,
os.path.join(app_path, 'static/images/antibody.png'))
attach_picture(Cytotoxin,
x,
os.path.join(app_path, 'static/images/cytotoxin.png'))
attach_picture(Adc,
x,
os.path.join(app_path, 'static/images/adc.png'))
print 'Database Populated'