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()
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()
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()
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)
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)
def create_user(login_session):
"""
Create a new user in the db using user info in the login_session
"""
new_user = User(name=login_session["username"], email=login_session["email"])
session.add(new_user)
session.commit()
user = session.query(User).filter_by(email=login_session["email"]).one()
attach_picture_url(User, user.id, login_session["picture"])
return user.id
def create_user(login_session):
"""
Create a new user in the db using user info in the login_session
"""
new_user = User(name=login_session['username'],
email=login_session['email'])
session.add(new_user)
session.commit()
user = session.query(User).filter_by(email=login_session['email']).one()
attach_picture_url(User, user.id, login_session['picture'])
return user.id
def edit_type_lot(dbtype, item_id):
"""Edit item within the category in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
abort(401)
# query the item user wants to edit
edit_item = (session.query(eval(dbtype.capitalize() +
'Lot')).filter_by(id=item_id).one())
# make sure user is authorized to edit this item
if login_session['user_id'] != edit_item.user_id:
flash('You are not authorized to modify items you did not create. '
'Please create your own item in order to modify it.')
return redirect(url_for(dbtype))
# get property names from table, check maximum lot# from ab and cytotoxin
table = Table('%s_lot' % dbtype, meta, autoload=True, autoload_with=engine)
max_ab_lot = (session.query(AntibodyLot).order_by(desc(
AntibodyLot.id)).first().id)
max_cytotoxin_lot = (session.query(CytotoxinLot).order_by(
desc(CytotoxinLot.id)).first().id)
if request.method == 'POST':
# set date attribute of query object with request form data
try:
edit_item.date = (datetime.strptime(
request.form['date'].replace('-', ' '), '%Y %m %d'))
# in some cases users can input 6 digit year, catch this error
except ValueError as detail:
print 'Handling run-time error: ', detail
flash('Invalid date detected. Please type the date in '
'format: MM/DD/YYYY')
return redirect(url_for(dbtype))
for column in table.columns:
if column.name in ('id', 'date', 'antibody_id', 'cytotoxin_id',
'adc_id', 'user_id'):
pass # don't modify item identifier
# set attribute of query object with request form data
else:
setattr(edit_item, column.name, request.form[column.name])
session.add(edit_item)
session.commit()
flash('%s Lot Edited' % dbtype.capitalize())
return redirect(url_for(dbtype))
else:
return render_template('edit-type-lot.html',
dbtype=dbtype,
columns=table.columns,
item_id=item_id,
edit_item=edit_item,
max_ab_lot=max_ab_lot,
max_cytotoxin_lot=max_cytotoxin_lot)
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 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 edit_type_lot(dbtype, item_id):
"""Edit item within the category in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
abort(401)
# query the item user wants to edit
edit_item = (session.query(eval(dbtype.capitalize()+'Lot'))
.filter_by(id=item_id).one())
# make sure user is authorized to edit this item
if login_session['user_id'] != edit_item.user_id:
flash('You are not authorized to modify items you did not create. '
'Please create your own item in order to modify it.')
return redirect(url_for(dbtype))
# get property names from table, check maximum lot# from ab and cytotoxin
table = Table('%s_lot' % dbtype, meta, autoload=True, autoload_with=engine)
max_ab_lot = (session.query(AntibodyLot)
.order_by(desc(AntibodyLot.id)).first().id)
max_cytotoxin_lot = (session.query(CytotoxinLot)
.order_by(desc(CytotoxinLot.id)).first().id)
if request.method == 'POST':
# set date attribute of query object with request form data
try:
edit_item.date = (datetime
.strptime(request
.form['date']
.replace('-', ' '), '%Y %m %d'))
# in some cases users can input 6 digit year, catch this error
except ValueError as detail:
print 'Handling run-time error: ', detail
flash('Invalid date detected. Please type the date in '
'format: MM/DD/YYYY')
return redirect(url_for(dbtype))
for column in table.columns:
if column.name in ('id', 'date', 'antibody_id',
'cytotoxin_id', 'adc_id', 'user_id'):
pass # don't modify item identifier
# set attribute of query object with request form data
else:
setattr(edit_item, column.name, request.form[column.name])
session.add(edit_item)
session.commit()
flash('%s Lot Edited' % dbtype.capitalize())
return redirect(url_for(dbtype))
else:
return render_template('edit-type-lot.html', dbtype=dbtype,
columns=table.columns, item_id=item_id,
edit_item=edit_item, max_ab_lot=max_ab_lot,
max_cytotoxin_lot=max_cytotoxin_lot)
def create_type_lot(dbtype, item_id):
"""Create new item within the category in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
return redirect(url_for(dbtype))
# get property names from table, check maximum lot# from ab and cytotoxin
table = Table('%s_lot' % dbtype, meta, autoload=True, autoload_with=engine)
max_ab_lot = (session.query(AntibodyLot)
.order_by(desc(AntibodyLot.id)).first().id)
max_cytotoxin_lot = (session.query(CytotoxinLot)
.order_by(desc(CytotoxinLot.id)).first().id)
origin_id = (session.query(eval(dbtype.capitalize()))
.filter_by(id=item_id).one().user_id)
user_id = get_user_id(login_session['email'])
if request.method == 'POST':
# instantiate new object
new = eval(dbtype.capitalize()+'Lot')()
for field in request.form:
# set date attribute of new object with request form data
if field == 'date':
try:
setattr(new,
field,
(datetime
.strptime(request
.form[field]
.replace('-', ' '), '%Y %m %d')))
# in some cases users can input 6 digit year, catch this error
except ValueError as detail:
print 'Handling run-time error: ', detail
flash('Invalid date detected. Please type the date in '
'format: MM/DD/YYYY')
return redirect(url_for(dbtype))
# set attribute of new object with request form data
if hasattr(new, field):
setattr(new, field, request.form[field])
setattr(new, dbtype+'_id', item_id)
setattr(new, 'user_id', user_id)
session.add(new)
session.commit()
flash('%s Lot Created' % dbtype.capitalize())
return redirect(url_for(dbtype))
else:
return render_template('create-type-lot.html', dbtype=dbtype,
columns=table.columns, item_id=item_id,
max_ab_lot=max_ab_lot,
max_cytotoxin_lot=max_cytotoxin_lot,
origin_id=origin_id,
user_id=get_user_id(login_session['email']))
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_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_type_lot(dbtype, item_id):
"""Create new item within the category in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
return redirect(url_for(dbtype))
# get property names from table, check maximum lot# from ab and cytotoxin
table = Table('%s_lot' % dbtype, meta, autoload=True, autoload_with=engine)
max_ab_lot = (session.query(AntibodyLot).order_by(desc(
AntibodyLot.id)).first().id)
max_cytotoxin_lot = (session.query(CytotoxinLot).order_by(
desc(CytotoxinLot.id)).first().id)
origin_id = (session.query(eval(
dbtype.capitalize())).filter_by(id=item_id).one().user_id)
user_id = get_user_id(login_session['email'])
if request.method == 'POST':
# instantiate new object
new = eval(dbtype.capitalize() + 'Lot')()
for field in request.form:
# set date attribute of new object with request form data
if field == 'date':
try:
setattr(new, field, (datetime.strptime(
request.form[field].replace('-', ' '), '%Y %m %d')))
# in some cases users can input 6 digit year, catch this error
except ValueError as detail:
print 'Handling run-time error: ', detail
flash('Invalid date detected. Please type the date in '
'format: MM/DD/YYYY')
return redirect(url_for(dbtype))
# set attribute of new object with request form data
if hasattr(new, field):
setattr(new, field, request.form[field])
setattr(new, dbtype + '_id', item_id)
setattr(new, 'user_id', user_id)
session.add(new)
session.commit()
flash('%s Lot Created' % dbtype.capitalize())
return redirect(url_for(dbtype))
else:
return render_template('create-type-lot.html',
dbtype=dbtype,
columns=table.columns,
item_id=item_id,
max_ab_lot=max_ab_lot,
max_cytotoxin_lot=max_cytotoxin_lot,
origin_id=origin_id,
user_id=get_user_id(login_session['email']))
def edit_type(dbtype, item_id):
"""Edit the category (within 3 pre-defined type) in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
abort(401)
# query the item user wants to edit
edit_item = (session.query(eval(
dbtype.capitalize())).filter_by(id=item_id).one())
# make sure user is authorized to edit this item
if login_session['user_id'] != edit_item.user_id:
flash('You are not authorized to modify items you did not create. '
'Please create your own item in order to modify it.')
return redirect(url_for(dbtype))
# get property names from table
table = Table(dbtype, meta, autoload=True, autoload_with=engine)
if request.method == 'POST':
for column in table.columns:
if column.name in ('id', 'user_id'):
pass # don't modify item id# and user_id#
else:
# set attribute of query object with request form data
setattr(edit_item, column.name, request.form[column.name])
session.add(edit_item)
session.commit()
flash('%s Edited' % dbtype.capitalize())
# upload image
image = request.files['picture']
if image and allowed_file(image.filename):
with store_context(fs_store):
edit_item.picture.from_file(image)
# prevent user uploading unsupported file type
elif image and not allowed_file(image.filename):
flash('Unsupported file detected. No image has been uploaded.')
return redirect(url_for(dbtype))
else:
return render_template('edit-type.html',
dbtype=dbtype,
columns=table.columns,
item_id=item_id,
edit_item=edit_item)
def edit_type(dbtype, item_id):
"""Edit the category (within 3 pre-defined type) in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
abort(401)
# query the item user wants to edit
edit_item = (session.query(eval(dbtype.capitalize()))
.filter_by(id=item_id).one())
# make sure user is authorized to edit this item
if login_session['user_id'] != edit_item.user_id:
flash('You are not authorized to modify items you did not create. '
'Please create your own item in order to modify it.')
return redirect(url_for(dbtype))
# get property names from table
table = Table(dbtype, meta, autoload=True, autoload_with=engine)
if request.method == 'POST':
for column in table.columns:
if column.name in ('id', 'user_id'):
pass # don't modify item id# and user_id#
else:
# set attribute of query object with request form data
setattr(edit_item, column.name, request.form[column.name])
session.add(edit_item)
session.commit()
flash('%s Edited' % dbtype.capitalize())
# upload image
image = request.files['picture']
if image and allowed_file(image.filename):
with store_context(fs_store):
edit_item.picture.from_file(image)
# prevent user uploading unsupported file type
elif image and not allowed_file(image.filename):
flash('Unsupported file detected. No image has been uploaded.')
return redirect(url_for(dbtype))
else:
return render_template('edit-type.html', dbtype=dbtype,
columns=table.columns, item_id=item_id,
edit_item=edit_item)
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()
def create_type(dbtype):
"""
Create new category (within 3 pre-defined type) in the database
"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
return redirect(url_for(dbtype))
# get property names from table
table = Table(dbtype, meta, autoload=True, autoload_with=engine)
user_id = get_user_id(login_session['email'])
if request.method == 'POST':
# instantiate new object
new = eval(dbtype.capitalize())()
for field in request.form:
# set attribute of new object with request form data
if hasattr(new, field):
setattr(new, field, request.form[field])
setattr(new, 'user_id', user_id)
session.add(new)
session.commit()
flash('%s Created' % dbtype.capitalize())
# upload image
image = request.files['picture']
if image and allowed_file(image.filename):
with store_context(fs_store):
new.picture.from_file(image)
# prevent user uploading unsupported file type
elif image and not allowed_file(image.filename):
flash('Unsupported file detected. No image has been uploaded.')
return redirect(url_for(dbtype))
else:
return render_template('create-type.html',
columns=table.columns,
dbtype=dbtype)
def create_type(dbtype):
"""
Create new category (within 3 pre-defined type) in the database
"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
return redirect(url_for(dbtype))
# get property names from table
table = Table(dbtype, meta, autoload=True, autoload_with=engine)
user_id = get_user_id(login_session['email'])
if request.method == 'POST':
# instantiate new object
new = eval(dbtype.capitalize())()
for field in request.form:
# set attribute of new object with request form data
if hasattr(new, field):
setattr(new, field, request.form[field])
setattr(new, 'user_id', user_id)
session.add(new)
session.commit()
flash('%s Created' % dbtype.capitalize())
# upload image
image = request.files['picture']
if image and allowed_file(image.filename):
with store_context(fs_store):
new.picture.from_file(image)
# prevent user uploading unsupported file type
elif image and not allowed_file(image.filename):
flash('Unsupported file detected. No image has been uploaded.')
return redirect(url_for(dbtype))
else:
return render_template('create-type.html',
columns=table.columns, dbtype=dbtype)
def save(self):
session.add(self)
session.commit()