def createADCLot():
lot = [1, 2, 3, 4, 5]
for x in range(20):
error = True
while error:
randomlot = choice(lot)
try:
id1 = choice(antibodylot()[randomlot-1])
id2 = choice(cytotoxinlot()[randomlot-1])
except IndexError:
lot.remove(randomlot)
else:
error = False
adclot = AdcLot(date=createRandomDate(),
aggregate=randint(0, 5)+round(random(), 2),
endotoxin=randint(0, 10)+round(random(), 2),
concentration=randint(0, 10)+round(random(), 2),
vialVolume=choice([1, 0.2, 0.5]),
vialNumber=randint(1, 100),
adc_id=randomlot,
antibodylot_id=id1,
cytotoxinlot_id=id2,
user_id=randint(1, 3))
session.add(adclot)
session.commit()
def createCytotoxin(): cytotoxin1 = Cytotoxin(name='Maytansine', weight=692.19614, drugClass='tubulin inhibitor', user_id=1) cytotoxin2 = Cytotoxin(name='Monomethyl auristatin E', weight=717.97858, drugClass='antineoplastic agent', user_id=2) cytotoxin3 = Cytotoxin(name='Calicheamicin', weight=1368.34, drugClass='enediyne antitumor antibotics', user_id=3) cytotoxin4 = Cytotoxin(name='Mertansine', weight=477.47, drugClass='tubulin inhibitor', user_id=1) cytotoxin5 = Cytotoxin(name='Pyrrolobenzodiazepine', weight=25827, drugClass='DNA crosslinking agent', user_id=2) session.add_all([cytotoxin1, cytotoxin2, cytotoxin3, cytotoxin4, cytotoxin5]) session.commit()
def createADC():
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 createUser(login_session):
"""Create a new user in the db using user info in the login_session"""
newUser = User(name=login_session['username'], email=login_session[
'email'])
session.add(newUser)
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 createUser(name, email, picture):
user = User(name=name, email=email)
session.add(user)
session.commit()
newUserID = session.query(User).filter_by(email=email).one().id
if picture.startswith("https"):
attach_picture_url(User, newUserID, picture)
else:
attach_picture(User, newUserID, picture)
def createCytotoxinLot():
for x in range(20):
cytotoxinlot = CytotoxinLot(date=createRandomDate(),
purity=randint(80, 99)+round(random(), 2),
concentration=randint(0,10)+round(random(), 2),
vialVolume=choice([1, 0.2, 0.5]),
vialNumber=randint(1, 100),
cytotoxin_id=randint(1, 5),
user_id=randint(1, 3))
session.add(cytotoxinlot)
session.commit()
def createAntibodyLot():
for x in range(20):
antibodylot = AntibodyLot(
date=createRandomDate(),
aggregate=randint(0, 5)+round(random(), 2),
endotoxin=randint(0, 10)+round(random(), 2),
concentration=randint(0, 10)+round(random(), 2),
vialVolume=choice([1, 0.2, 0.5]),
vialNumber=randint(1, 100),
antibody_id=randint(1, 5),
user_id=randint(1, 3))
session.add(antibodylot)
session.commit()
def editTypeLot(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
editedItem = (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'] != editedItem.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)
maxablot = (session.query(AntibodyLot)
.order_by(desc(AntibodyLot.id)).first().id)
maxtoxinlot = (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:
editedItem.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(editedItem, column.name, request.form[column.name])
session.add(editedItem)
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,
editedItem=editedItem, maxablot=maxablot,
maxtoxinlot=maxtoxinlot)
def createTypeLot(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)
maxablot = (session.query(AntibodyLot)
.order_by(desc(AntibodyLot.id)).first().id)
maxtoxinlot = (session.query(CytotoxinLot)
.order_by(desc(CytotoxinLot.id)).first().id)
originID = (session.query(eval(dbtype.capitalize()))
.filter_by(id=item_id).one().user_id)
user_id = getUserID(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,
maxablot=maxablot, maxtoxinlot=maxtoxinlot,
originID=originID,
userID=getUserID(login_session['email']))
def editType(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
editedItem = (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'] != editedItem.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(editedItem, column.name, request.form[column.name])
session.add(editedItem)
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):
editedItem.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,
editedItem=editedItem)
def attach_picture_url(table, item_id, location):
"""
A helper function used in populator.py to upload picture to the db from web
Args:
table: The category which the picture belongs to
item_id: The category's id number which the picture should be
uploaded to
location: a web url of where the picture is found
Returns:
None
"""
try:
item = session.query(table).filter_by(id=item_id).one()
with store_context(fs_store):
item.picture.from_file(urlopen(location))
session.commit()
except Exception:
session.rollback()
raise
def createAntibody():
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 delete(dbtype, item_id):
"""Delete either the item or 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 delete
deleteItem = (session.query(eval(dbtype[0].upper()+dbtype[1:]))
.filter_by(id=item_id).one())
# make sure user is authorized to delete this item
if login_session['user_id'] != deleteItem.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))
if request.method == 'POST':
try:
session.delete(deleteItem)
session.commit()
# handling legacy error when delete invovled cascade-delete
except IntegrityError as detail:
print 'Handling run-time error: ', detail
session.rollback()
flash('Delete Operation Failed')
return redirect(url_for('home'))
if dbtype.endswith('Lot'):
flash('%s Lot Deleted' % dbtype[:-3].capitalize())
return redirect(url_for(dbtype[:-3]))
else:
flash('%s Deleted' % dbtype.capitalize())
return redirect(url_for(dbtype))
else:
pass
def createType(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 = getUserID(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)