def register():
form = RegisterForm(request.form)
if form.validate_on_submit():
user = User(form.username.data, form.email.data, form.password.data,
form.type.data, False)
db.session.add(user)
db.session.commit()
temp = None
if form.type.data == 'Consumer':
temp = Consumer(ConsumerID=user.UserID)
elif form.type.data == 'Company':
temp = Company(CompanyID=user.UserID)
else:
temp = Designer(DesignerID=user.UserID)
db.session.add(temp)
db.session.commit()
token = generate_confirmation_token(user.UserEmail)
confirm_url = url_for('auth.confirm_email',
token=token,
_external=True)
html = render_template('auth/activate.html', confirm_url=confirm_url)
subject = "Please confirm your email"
send_email(user.UserEmail, subject, html)
login_user(user)
flash('A confirmation email has been sent via email.', 'success')
return redirect(url_for("auth.unconfirmed"))
return render_template('auth/register.html', form=form)
def export_posts(user_id):
try:
user = User.query.get(user_id)
_set_task_progress(0)
data = []
total_posts = user.posts.count()
for i, post in enumerate(user.posts.order_by(Post.timestamp.asc())):
data.append({
"body": post.body,
"timestamp": post.timestamp.isoformat() + "Z"
})
time.sleep(5) # Only needed to test out progress reporting
_set_task_progress(i / total_posts * 100)
# Send email to user
send_email(
subject="Your blog post export",
sender=app.config["ADMINS"][0],
recipients=[user.email],
text_body=render_template("email/export_posts.txt", user=user),
html_body=render_template("email/export_posts.html", user=user),
attachments=[(
"posts.json",
"application/json",
json.dumps({"posts": data}, indent=4),
)],
sync=True,
)
except:
app.logger.error("Unhandled exception", exc_info=sys.exc_info())
finally:
_set_task_progress(100)
def export_posts(user_id):
try:
user = User.query.get(user_id)
_set_task_progress(0)
data = []
total_posts = user.posts.count()
for i, post in enumerate(user.posts.order_by(Post.timestamp.asc())):
data.append({
'body': post.body,
'timestamp': post.timestamp.isoformat() + 'Z',
})
# for testing purposes, set a sleep to see task progress in web browser
time.sleep(5)
_set_task_progress(100 * i // total_posts)
send_email(
'[Microblog] Exported Posts',
sender=app.config['ADMINS'][0],
recipients=[user.email],
body=render_template('email/export_posts.txt', user=user),
html=render_template('email/export_posts.html', user=user),
attachments=[(
'posts.json',
'application/json',
json.dumps({'posts': data}, indent=4),
)],
sync=True,
)
except:
_set_task_progress(100)
app.logger.error('Unhandled exception', exc_info=sys.exc_info())
def export_posts(user_id):
try:
user = User.query.get(user_id)
_set_task_progress(0)
data = []
i = 0
total_posts = user.posts.count()
for post in user.posts.order_by(Post.timestamp.asc()):
data.append({
'body': post.body,
'timestamp': post.timestamp.isoformat() + 'Z'
})
time.sleep(5)
i += 1
_set_task_progress(100 * i // total_posts)
send_email('[Microblog] Your blog posts',
sender=app.config['MAIL_FROM'],
recipients=[user.email],
text_body=render_template('email/export_posts.txt',
user=user),
html_body=render_template('email/export_posts.html',
user=user),
attachments=[('posts.json', 'application/json',
json.dumps({'posts': data}, indent=4))],
sync=True)
except:
_set_task_progress(100)
app.logger.error('Unhandled exception', exc_info=sys.exc_info())
def reset_password_request():
title = 'Reset password'
if current_user.is_authenticated:
redirect(url_for('auth.index'))
form = StartResetPasswordForm()
if form.validate_on_submit():
if form.email_validate():
pass
else:
user = User.query.filter_by(email=form.email.data).first()
token = user.get_reset_password_token()
html_body = render_template('auth/reset_password.html',
user=user,
token=token)
send_email(subject='Сброс пароля',
sender='*****@*****.**',
recipients=[user.email],
html_body=html_body)
flash(f'Вам отправлено письмо на почту {user.email}')
return redirect(url_for('auth.reset_password_request'))
return render_template('auth/start_reset_password_form.html',
form=form,
title=title)
def export_posts(user_id):
# web应用中的错误和异常会有app.logger来收集，但是对于后台任务是一个单独的进程，所以需要手动来收集错误信息，否则只能通过worker的控制台才能看到错误
try:
_set_task_progress(0)
user = User.query.get(user_id)
total_post = user.posts.count()
data = []
i = 0
for post in user.posts.order_by(Post.timestamp.desc()).all():
data.append({'body': post.body,
'timestamp': post.timestamp.isoformat() + 'Z'}) # 把datetime格式的时间转换成字符串，最后加上时区
i += 1
time.sleep(3)
_set_task_progress(100*i/total_post)
email.send_email(subject='[myblog] your posts',
sender=app.config['ADMIN'],
receiver=[user.email],
text_body=render_template('auth/email/export_posts.txt', user=user),
html_body=render_template('auth/email/export_posts.html', user=user),
attachments=[('posts.txt', 'text/plain',
json.dumps({'posts': data}, ensure_ascii=False, indent=4).encode('utf-8'))],
# indent=4是为了更好看的输出, encode编码是为了保证附件的中文不被转换成16进制
sync=True) # 这里已经是后台任务，所以选择成同步模式发送邮件，否则会有问题
except:
_set_task_progress(100)
app.logger.error('Unhandled exception', exc_info=sys.exc_info()) # sys.exc_info()方法包含了错误的traceback信息
def email_patient(email):
form = EmailPatientForm()
if form.validate_on_submit():
#subject, sender, reciever, text_body, html_body
send_email(form.subject.data, current_user.email, email,
form.body.data, form.body.data)
flash('Your email has succesfully been sent.')
return redirect(url_for('auth.all_patients', email=current_user.email))
return render_template('auth/email_patient.html', email=email, form=form)
def signup():
"""
Signup a user using name, email, password.
:return: Http Json response
"""
if request.content_type == 'application/json':
post_data = request.get_json(force=True)
email = post_data.get('email')
password = User.encode_password(post_data.get('password'))
name = post_data.get('name')
if re.match(r"[^@]+@[^@]+\.[^@]+", email):
user = User.get_by_email(email)
if user and user.isActive and user.isEmailVerified:
return response(
'failed',
'Email already registered. Use the Sign-in option', 401)
if user and user.isActive and not user.isEmailVerified:
token = user.get_auth_token()
confirm_url = url_for('auth.verify',
token=token,
_external=True)
html = render_template('activate.html',
confirm_url=confirm_url)
subject = "Fronteous Arena - Confirm your email address"
send_email(user.email_id, subject, html)
logger.bind(userId=user._id)
return response_auth('success', 'Successfully signed up.',
None, None, 200)
else:
user = User(email_id=email, name=name, password=password)
user.sign_up(userObj=post_data)
if not user.isEmailVerified: #If email is not verified. Not email at this stage wil be verified only for invited users coming through invitation token
token = user.get_auth_token()
confirm_url = url_for('auth.verify',
token=token,
_external=True)
html = render_template('activate.html',
confirm_url=confirm_url)
subject = "Fronteous Arena - Confirm your email address"
send_email(user.email_id, subject, html)
logger.bind(userId=user._id)
return response_auth('success', 'Successfully signed up.',
None, None, 200)
return response(
'failed',
'Missing or wrong email format or password is less than four characters',
400)
return response('failed', 'Content-type must be json', 402)
def signup():
if current_user.is_authenticated:
return redirect(url_for('main.index'))
# jsonify({'url': '/', 'msg': 'you are already login, you cant perform this action'})
form = RegistrationForm(request.form)
if request.method == 'POST':
if form.validate_on_submit():
# noinspection PyArgumentList,PyArgumentList,PyArgumentList,PyArgumentList,PyArgumentList,PyArgumentList
user = User(full_name=request.form['full_name'],
email=request.form['email'],
username=request.form['username'],
password=request.form['password'],
email_confirmed=False,
account_confirmed=False)
try:
db.session.add(user)
db.session.commit()
except IntegrityError:
db.session.rollback()
# The following lines of code
# is the confirmation email being sent
# to the user
token = generate_confirmation_token(user.email)
confirm_url = url_for('auth.confirm_email',
token=token,
_external=True)
html = render_template('activate.html', confirm_url=confirm_url)
subject = 'Please confirm your Email'
# send_email function was imported from
# the email file
#
send_email(user.email, subject, html)
flash('A mail has been sent to you')
return redirect(url_for('auth.login'))
# return jsonify({'code': 200, 'url': '/login'})
# else:
# return jsonify({'msg': 'something wrong occurred', 'url': '/signup'})
return render_template('register.html', form=form)
def post(self):
parser = reqparse.RequestParser()
parser.add_argument('username', required=True)
parser.add_argument('email', required=True)
parser.add_argument('password', required=True)
args = parser.parse_args()
# 验证长度
if len(args['username']) == 0 or len(args['username']) > 32:
abort_unacceptable_length("username")
if len(args['email']) == 0:
abort_unacceptable_length("email")
if len(args['password']) == 0:
abort_unacceptable_length("password")
# User existing
if LocalAuth.query.filter_by(username=args['username']).first():
abort_username_existed('username')
if LocalAuth.query.filter_by(email=args['email']).first():
abort_username_existed('email')
# 写入数据库
user = User()
db.session.add(user)
db.session.commit()
localauth = LocalAuth(username=args['username'],
email=args['email'],
user=user)
localauth.hash_password(args['password'])
db.session.add(localauth)
db.session.commit()
# 发送邮件
token = generate_confirmation_token(localauth.email)
confirm_url = url_for('frontend.confirm_email',
token=token,
_external=True)
html = '''
<p>Welcome! Thanks for signing up. Please follow this link to activate your account:</p>
<p><a href="%s">%s</a></p>
<br>
<p>Cheers!</p>
''' % (confirm_url, confirm_url)
subject = "Please confirm your email"
send_email(localauth.email, subject, html)
return "{ 'username': %s }" % (localauth.username), 201
def login():
if current_user.is_authenticated:
return redirect(url_for('main.index'))
form = LoginForm()
if form.validate_on_submit():
user = User.query.filter_by(username=form.username.data).first()
if user is None or not user.check_password(form.password.data):
flash("Invalid user name or password")
return redirect(url_for('auth.login'))
login_user(user, remember=form.remember_me.data)
send_email('new message from Hello', '*****@*****.**',
['*****@*****.**'], 'this is body',
'this is html body')
next_page = request.args.get('next')
if not next_page or url_parse(next_page).netloc != '':
next_page = url_for("main.index")
return redirect(next_page)
return render_template('auth/login.html', form=form, title="Sign In")
def reset():
if current_user.is_authenticated:
return redirect(url_for('main.index'))
form = EmailForm(request.form)
if request.method == 'POST':
if form.validate_on_submit():
user = User.query.filter_by(email=request.form['email']).first()
if user and user.email_confirmed:
subject = 'Password reset requested'
token = generate_recovery_token(user.email)
recover_url = url_for('auth.reset_password_with_token',
token=token,
_external=True)
html = render_template('recover.html', recover_url=recover_url)
send_email(user.email, subject, html)
flash(
'A confirmation link to reset your password has been sent to you'
)
return redirect(url_for('auth.login'))
# return jsonify({'url': '/login'})
else:
flash('This email has\nt been confirmed yet')
# return jsonify({'msg': 'This email has\nt been confirmed yet'})
return render_template('reset.html', form=form)
def resend_email():
if current_user.is_authenticated:
return jsonify({'url': '/', 'msg': 'user already logged in'})
form = ResendEmailForm(request.form)
if request.method == 'POST':
if form.validate_on_submit():
user = User.query.filter_by(email=request.form['email']).first()
token = resend_confirmation_token(user.email)
subject = 'Please confirm your email'
confirm_url = url_for('auth.confirm_recovery_email',
token=token,
_external=True)
html = render_template('resend_email_confirms.html',
confirm_url=confirm_url)
send_email(user.email, subject, html)
flash('A confirmation email has been sent to you')
return redirect(url_for('main.index'))
# return jsonify({'url': '/login'})
# else:
# return jsonify({'status': 'error','msg': 'check post form',
# 'url': '/resend/email'})
return render_template('resend_email.html', form=form)
def submission():
user = load_user(current_user.id)
query_seq = Post(author=user).query.order_by(Post.timestamp.desc()).first()
query_seq = query_seq.body
hasher = hashlib.md5(query_seq.encode('ASCII'))
hasher = hasher.hexdigest()[:50]
hasher = hasher + str(random.randint(1, 10000))
sequence = '/Users/LarryBliss/Documents/Viper 2/Hermes_Prediction/app/backend/Sequences_for_prediction.fa'
with open(sequence, 'w') as outfile:
outfile.write(str(query_seq))
with open(sequence, 'a') as outfile:
with open(sequence, 'r') as fin:
lines = fin.readlines()
# flash(lines[-1])
if lines[-1] != '>':
outfile.write('\n>\n')
sequences = []
with open(sequence, 'r') as fin:
in_sequence = ''
for line in fin:
if line.startswith('>'):
sequences.append(in_sequence)
in_sequence = ''
else:
in_sequence += line.strip()
# flash(sequences)
sequences = list(filter(None, sequences))
# flash(sequences)
# flash(query_seq)
prediction_sets = []
title_set = []
dummy_email_list = [
'*****@*****.**', '*****@*****.**',
'*****@*****.**', '*****@*****.**',
'*****@*****.**', '*****@*****.**',
'*****@*****.**', '*****@*****.**',
'*****@*****.**', '*****@*****.**',
'*****@*****.**', '*****@*****.**',
'*****@*****.**'
]
for seq, dummy_email in zip(sequences, itertools.cycle(dummy_email_list)):
DNA, RNA, protein, protein_length, Hermes_final_solution = Launcher(
dummy_email, seq)
prediction_sets.append(
[DNA, RNA, protein, protein_length, Hermes_final_solution])
title_set.append([
'DNA sequence: ', 'RNA sequence: ', 'Amino acid sequence: ',
'Length of the protein: ', 'Final Hermes_Prediction Solution: '
])
if Hermes_final_solution == "":
flash(
"Unfortunately there is an issue with a protein layer server and an optimal result is unattainable at this momment, please try again later"
)
count = 1
message = ""
with open(
"/Users/LarryBliss/Documents/Viper 2/Hermes_Prediction/app/solved_prediction_set.txt",
'w') as prediction_file:
for pred_set, t_set in zip(prediction_sets, title_set):
prediction_file.write("Submission " + str(count) + '\n')
message += "Submission " + str(count) + '\n'
message += '\n'
for element1, element2 in zip(pred_set, t_set):
prediction_file.write(str(element2))
prediction_file.write(str(element1) + '\n')
message += '\n'
message += str(element2)
message += str(element1) + '\n'
count += 1
with open(
"/Users/LarryBliss/Documents/Viper 2/Hermes_Prediction/app/templates/base_prediction.html",
'r') as base_file:
with open(
"/Users/LarryBliss/Documents/Viper 2/Hermes_Prediction/app/templates/prediction.html",
"w") as final_file:
lines = base_file.readlines()
for line in lines:
final_file.write(line)
with open(
"/Users/LarryBliss/Documents/Viper 2/Hermes_Prediction/app/solved_prediction_set.txt",
"r") as contents:
with open(
"/Users/LarryBliss/Documents/Viper 2/Hermes_Prediction/app/templates/prediction.html",
"a") as e:
for lines in contents.readlines():
if lines != '\n' or lines != None:
e.write('<pre style="font-size:18px">' + lines +
"</pre> <br>\n")
e.write("{% endblock %}")
send_email(user.email, message)
return redirect(url_for('main.specific_submission', hasher=hasher))
