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)