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https://gitlab.ub.uni-bielefeld.de/sfb1288inf/nopaque.git
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671 lines
24 KiB
Python
671 lines
24 KiB
Python
from datetime import datetime
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from flask import current_app
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from flask_login import UserMixin, AnonymousUserMixin
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from itsdangerous import BadSignature, TimedJSONWebSignatureSerializer
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from time import sleep
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from werkzeug.security import generate_password_hash, check_password_hash
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from werkzeug.utils import secure_filename
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import xml.etree.ElementTree as ET
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from . import db, login_manager
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import os
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import shutil
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class Permission:
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'''
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Defines User permissions as integers by the power of 2. User permission
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can be evaluated using the bitwise operator &. 3 equals to CREATE_JOB and
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DELETE_JOB and so on.
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'''
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MANAGE_CORPORA = 1
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MANAGE_JOBS = 2
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# PERMISSION_NAME = 4
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# PERMISSION_NAME = 8
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ADMIN = 16
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class Role(db.Model):
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'''
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Model for the different roles Users can have. Is a one-to-many
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relationship. A Role can be associated with many User rows.
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'''
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__tablename__ = 'roles'
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# Primary key
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id = db.Column(db.Integer, primary_key=True)
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# Fields
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default = db.Column(db.Boolean, default=False, index=True)
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name = db.Column(db.String(64), unique=True)
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permissions = db.Column(db.BigInteger)
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# Relationships
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users = db.relationship('User', backref='role', lazy='dynamic')
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def to_dict(self):
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return {'id': self.id,
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'default': self.default,
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'name': self.name,
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'permissions': self.permissions}
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def __init__(self, **kwargs):
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super(Role, self).__init__(**kwargs)
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if self.permissions is None:
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self.permissions = 0
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def __repr__(self):
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'''
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String representation of the Role. For human readability.
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'''
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return '<Role {role_name}>'.format(role_name=self.name)
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def add_permission(self, perm):
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'''
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Add new permission to Role. Input is a Permission.
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'''
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if not self.has_permission(perm):
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self.permissions += perm
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def remove_permission(self, perm):
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'''
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Removes permission from a Role. Input a Permission.
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'''
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if self.has_permission(perm):
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self.permissions -= perm
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def reset_permissions(self):
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'''
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Resets permissions to zero. Zero equals no permissions at all.
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'''
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self.permissions = 0
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def has_permission(self, perm):
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'''
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Checks if a Role has a specific Permission. Does this with the bitwise
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operator.
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'''
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return self.permissions & perm == perm
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@staticmethod
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def insert_roles():
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'''
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Inserts roles into the database. This has to be executed befor Users
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are added to the database. Otherwiese Users will not have a Role
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assigned to them. Order of the roles dictionary determines the ID of
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each role. Users have the ID 1 and Administrators have the ID 2.
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'''
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roles = {'User': [Permission.MANAGE_CORPORA, Permission.MANAGE_JOBS],
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'Administrator': [Permission.MANAGE_CORPORA,
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Permission.MANAGE_JOBS, Permission.ADMIN]}
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default_role = 'User'
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for r in roles:
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role = Role.query.filter_by(name=r).first()
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if role is None:
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role = Role(name=r)
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role.reset_permissions()
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for perm in roles[r]:
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role.add_permission(perm)
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role.default = (role.name == default_role)
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db.session.add(role)
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db.session.commit()
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class User(UserMixin, db.Model):
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'''
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Model for Users that are registered to Opaque.
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'''
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__tablename__ = 'users'
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# Primary key
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id = db.Column(db.Integer, primary_key=True)
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# Foreign keys
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role_id = db.Column(db.Integer, db.ForeignKey('roles.id'))
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# Fields
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confirmed = db.Column(db.Boolean, default=False)
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email = db.Column(db.String(254), unique=True, index=True)
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last_seen = db.Column(db.DateTime(), default=datetime.utcnow)
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member_since = db.Column(db.DateTime(), default=datetime.utcnow)
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password_hash = db.Column(db.String(128))
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setting_dark_mode = db.Column(db.Boolean, default=False)
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setting_job_status_mail_notifications = db.Column(db.String(16),
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default='end')
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setting_job_status_site_notifications = db.Column(db.String(16),
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default='all')
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username = db.Column(db.String(64), unique=True, index=True)
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# Relationships
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corpora = db.relationship('Corpus', backref='creator', lazy='dynamic',
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cascade='save-update, merge, delete')
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jobs = db.relationship('Job', backref='creator', lazy='dynamic',
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cascade='save-update, merge, delete')
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query_results = db.relationship('QueryResult',
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backref='creator',
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cascade='save-update, merge, delete',
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lazy='dynamic')
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def to_dict(self):
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return {'id': self.id,
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'role_id': self.role_id,
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'confirmed': self.confirmed,
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'email': self.email,
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'last_seen': self.last_seen.timestamp(),
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'member_since': self.member_since.timestamp(),
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'username': self.username,
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'settings': {'dark_mode': self.setting_dark_mode,
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'job_status_mail_notifications':
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self.setting_job_status_mail_notifications,
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'job_status_site_notifications':
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self.setting_job_status_site_notifications},
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'corpora': {corpus.id: corpus.to_dict()
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for corpus in self.corpora},
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'jobs': {job.id: job.to_dict() for job in self.jobs},
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'query_results': {query_result.id: query_result.to_dict()
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for query_result in self.query_results}}
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def __repr__(self):
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'''
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String representation of the User. For human readability.
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'''
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return '<User {username}>'.format(username=self.username)
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def __init__(self, **kwargs):
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super(User, self).__init__(**kwargs)
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if self.role is None:
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if self.email == current_app.config['NOPAQUE_ADMIN']:
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self.role = Role.query.filter_by(name='Administrator').first()
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if self.role is None:
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self.role = Role.query.filter_by(default=True).first()
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def generate_confirmation_token(self, expiration=3600):
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'''
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Generates a confirmation token for user confirmation via email.
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'''
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s = TimedJSONWebSignatureSerializer(current_app.config['SECRET_KEY'],
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expiration)
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return s.dumps({'confirm': self.id}).decode('utf-8')
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def generate_reset_token(self, expiration=3600):
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'''
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Generates a reset token for password reset via email.
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'''
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s = TimedJSONWebSignatureSerializer(current_app.config['SECRET_KEY'],
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expiration)
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return s.dumps({'reset': self.id}).decode('utf-8')
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def confirm(self, token):
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'''
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Confirms User if the given token is valid and not expired.
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'''
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s = TimedJSONWebSignatureSerializer(current_app.config['SECRET_KEY'])
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try:
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data = s.loads(token.encode('utf-8'))
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except BadSignature:
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return False
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if data.get('confirm') != self.id:
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return False
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self.confirmed = True
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db.session.add(self)
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return True
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@staticmethod
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def reset_password(token, new_password):
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'''
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Resets password for User if the given token is valid and not expired.
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'''
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s = TimedJSONWebSignatureSerializer(current_app.config['SECRET_KEY'])
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try:
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data = s.loads(token.encode('utf-8'))
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except BadSignature:
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return False
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user = User.query.get(data.get('reset'))
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if user is None:
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return False
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user.password = new_password
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db.session.add(user)
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return True
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@property
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def password(self):
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raise AttributeError('password is not a readable attribute')
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@password.setter
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def password(self, password):
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self.password_hash = generate_password_hash(password)
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def verify_password(self, password):
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return check_password_hash(self.password_hash, password)
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def can(self, perm):
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'''
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Checks if a User with its current role can doe something. Checks if the
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associated role actually has the needed Permission.
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'''
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return self.role is not None and self.role.has_permission(perm)
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def is_administrator(self):
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'''
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Checks if User has Admin permissions.
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'''
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return self.can(Permission.ADMIN)
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def ping(self):
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self.last_seen = datetime.utcnow()
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db.session.add(self)
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def delete(self):
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'''
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Delete the user and its corpora and jobs from database and filesystem.
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'''
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user_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
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str(self.id))
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shutil.rmtree(user_dir, ignore_errors=True)
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db.session.delete(self)
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class AnonymousUser(AnonymousUserMixin):
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'''
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Model replaces the default AnonymousUser.
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'''
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def can(self, permissions):
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return False
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def is_administrator(self):
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return False
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class JobInput(db.Model):
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'''
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Class to define JobInputs.
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'''
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__tablename__ = 'job_inputs'
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# Primary key
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id = db.Column(db.Integer, primary_key=True)
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# Foreign keys
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job_id = db.Column(db.Integer, db.ForeignKey('jobs.id'))
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# Fields
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dir = db.Column(db.String(255))
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filename = db.Column(db.String(255))
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def __repr__(self):
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'''
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String representation of the JobInput. For human readability.
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'''
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return '<JobInput {filename}>'.format(filename=self.filename)
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def to_dict(self):
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return {'id': self.id,
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'job_id': self.job_id,
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'filename': self.filename}
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class JobResult(db.Model):
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'''
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Class to define JobResults.
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'''
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__tablename__ = 'job_results'
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# Primary key
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id = db.Column(db.Integer, primary_key=True)
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# Foreign keys
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job_id = db.Column(db.Integer, db.ForeignKey('jobs.id'))
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# Fields
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dir = db.Column(db.String(255))
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filename = db.Column(db.String(255))
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def __repr__(self):
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'''
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String representation of the JobResult. For human readability.
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'''
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return '<JobResult {filename}>'.format(filename=self.filename)
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def to_dict(self):
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return {'id': self.id,
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'job_id': self.job_id,
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'filename': self.filename}
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class Job(db.Model):
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'''
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Class to define Jobs.
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'''
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__tablename__ = 'jobs'
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# Primary key
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id = db.Column(db.Integer, primary_key=True)
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# Foreign keys
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user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
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# Fields
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creation_date = db.Column(db.DateTime(), default=datetime.utcnow)
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description = db.Column(db.String(255))
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end_date = db.Column(db.DateTime())
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mem_mb = db.Column(db.Integer)
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n_cores = db.Column(db.Integer)
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secure_filename = db.Column(db.String(32))
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service = db.Column(db.String(64))
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'''
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' Service specific arguments as string list.
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' Example: ["-l eng", "--binarize"]
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'''
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service_args = db.Column(db.String(255))
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service_version = db.Column(db.String(16))
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status = db.Column(db.String(16))
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title = db.Column(db.String(32))
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# Relationships
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inputs = db.relationship('JobInput', backref='job', lazy='dynamic',
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cascade='save-update, merge, delete')
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results = db.relationship('JobResult', backref='job', lazy='dynamic',
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cascade='save-update, merge, delete')
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notification_data = db.relationship('NotificationData',
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cascade='save-update, merge, delete',
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uselist=False,
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back_populates='job') # One-to-One relationship
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notification_email_data = db.relationship('NotificationEmailData',
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cascade='save-update, merge, delete',
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back_populates='job')
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def __repr__(self):
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'''
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String representation of the Job. For human readability.
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'''
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return '<Job {job_title}>'.format(job_title=self.title)
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def create_secure_filename(self):
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'''
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Takes the job.title string nad cratesa a secure filename from this.
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'''
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self.secure_filename = secure_filename(self.title)
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def delete(self):
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'''
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Delete the job and its inputs and results from the database.
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'''
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if self.status not in ['complete', 'failed']:
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self.status = 'canceling'
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db.session.commit()
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while self.status != 'canceled':
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# In case the daemon handled a job in any way
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if self.status != 'canceling':
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self.status = 'canceling'
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db.session.commit()
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sleep(1)
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db.session.refresh(self)
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job_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
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str(self.user_id),
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'jobs',
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str(self.id))
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shutil.rmtree(job_dir, ignore_errors=True)
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db.session.delete(self)
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def restart(self):
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'''
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Restart a job - only if the status is failed
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'''
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if self.status != 'failed':
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raise Exception('Could not restart job: status is not "failed"')
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job_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
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str(self.user_id),
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'jobs',
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str(self.id))
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shutil.rmtree(os.path.join(job_dir, 'output'), ignore_errors=True)
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shutil.rmtree(os.path.join(job_dir, 'pyflow.data'), ignore_errors=True)
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self.end_date = None
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self.status = 'submitted'
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def to_dict(self):
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return {'id': self.id,
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'user_id': self.user_id,
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'creation_date': self.creation_date.timestamp(),
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'description': self.description,
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'end_date': (self.end_date.timestamp() if self.end_date else
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None),
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'inputs': {input.id: input.to_dict() for input in self.inputs},
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'mem_mb': self.mem_mb,
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'n_cores': self.n_cores,
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'results': {result.id: result.to_dict()
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for result in self.results},
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'service': self.service,
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'service_args': self.service_args,
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'service_version': self.service_version,
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'status': self.status,
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'title': self.title}
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class NotificationData(db.Model):
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'''
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Class to define notification data used for sending a notification mail with
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nopaque_notify.
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'''
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__tablename__ = 'notification_data'
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# Primary key
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id = db.Column(db.Integer, primary_key=True)
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# Foreign Key
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job_id = db.Column(db.Integer, db.ForeignKey('jobs.id'))
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# relationships
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job = db.relationship('Job', back_populates='notification_data')
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# Fields
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notified_on = db.Column(db.String(16), default=None)
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def __repr__(self):
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'''
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String representation of the NotificationData. For human readability.
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'''
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return '<NotificationData {id}>'.format(id=self.id)
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def to_dict(self):
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return {'id': self.id,
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'job_id': self.job_id,
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'job': self.job,
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'notified': self.notified}
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class NotificationEmailData(db.Model):
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'''
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Class to define data that will be used to send a corresponding Notification
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via email.
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'''
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__tablename__ = 'notification_email_data'
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# Primary Key
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id = db.Column(db.Integer, primary_key=True)
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# Foreign Key
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job_id = db.Column(db.Integer, db.ForeignKey('jobs.id'))
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# relationships
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job = db.relationship('Job', back_populates='notification_email_data')
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notify_status = db.Column(db.String(16), default=None)
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creation_date = db.Column(db.DateTime(), default=datetime.utcnow)
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def __repr__(self):
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'''
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String representation of the NotificationEmailData. For human readability.
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'''
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return '<NotificationData {id}>'.format(id=self.id)
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def to_dict(self):
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return {'id': self.id,
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'job_id': self.job_id,
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'job': self.job,
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'notify_status': self.notify_status,
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'creation_date': self.creation_date}
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class CorpusFile(db.Model):
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'''
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Class to define Files.
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'''
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__tablename__ = 'corpus_files'
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# Primary key
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id = db.Column(db.Integer, primary_key=True)
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# Foreign keys
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corpus_id = db.Column(db.Integer, db.ForeignKey('corpora.id'))
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# Fields
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address = db.Column(db.String(255))
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author = db.Column(db.String(255))
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booktitle = db.Column(db.String(255))
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chapter = db.Column(db.String(255))
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dir = db.Column(db.String(255))
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editor = db.Column(db.String(255))
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filename = db.Column(db.String(255))
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institution = db.Column(db.String(255))
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journal = db.Column(db.String(255))
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pages = db.Column(db.String(255))
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publisher = db.Column(db.String(255))
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publishing_year = db.Column(db.Integer)
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school = db.Column(db.String(255))
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title = db.Column(db.String(255))
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def delete(self):
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corpus_file_path = os.path.join(current_app.config['NOPAQUE_STORAGE'],
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str(self.corpus.user_id),
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'corpora',
|
||
str(self.corpus_id),
|
||
self.filename)
|
||
try:
|
||
os.remove(corpus_file_path)
|
||
except OSError:
|
||
pass
|
||
db.session.delete(self)
|
||
self.corpus.status = 'unprepared'
|
||
|
||
def to_dict(self):
|
||
return {'id': self.id,
|
||
'corpus_id': self.corpus_id,
|
||
'address': self.address,
|
||
'author': self.author,
|
||
'booktitle': self.booktitle,
|
||
'chapter': self.chapter,
|
||
'editor': self.editor,
|
||
'filename': self.filename,
|
||
'institution': self.institution,
|
||
'journal': self.journal,
|
||
'pages': self.pages,
|
||
'publisher': self.publisher,
|
||
'publishing_year': self.publishing_year,
|
||
'school': self.school,
|
||
'title': self.title}
|
||
|
||
|
||
class Corpus(db.Model):
|
||
'''
|
||
Class to define a corpus.
|
||
'''
|
||
__tablename__ = 'corpora'
|
||
# Primary key
|
||
id = db.Column(db.Integer, primary_key=True)
|
||
# Foreign keys
|
||
user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
|
||
# Fields
|
||
creation_date = db.Column(db.DateTime(), default=datetime.utcnow)
|
||
current_nr_of_tokens = db.Column(db.BigInteger, default=0)
|
||
description = db.Column(db.String(255))
|
||
last_edited_date = db.Column(db.DateTime(), default=datetime.utcnow)
|
||
max_nr_of_tokens = db.Column(db.BigInteger, default=2147483647)
|
||
status = db.Column(db.String(16))
|
||
title = db.Column(db.String(32))
|
||
# Relationships
|
||
files = db.relationship('CorpusFile', backref='corpus', lazy='dynamic',
|
||
cascade='save-update, merge, delete')
|
||
|
||
def to_dict(self):
|
||
return {'id': self.id,
|
||
'user_id': self.user_id,
|
||
'creation_date': self.creation_date.timestamp(),
|
||
'description': self.description,
|
||
'status': self.status,
|
||
'last_edited_date': self.last_edited_date.timestamp(),
|
||
'title': self.title,
|
||
'files': {file.id: file.to_dict() for file in self.files}}
|
||
|
||
def build(self):
|
||
corpus_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
|
||
str(self.user_id),
|
||
'corpora',
|
||
str(self.id))
|
||
output_dir = os.path.join(corpus_dir, 'merged')
|
||
shutil.rmtree(output_dir, ignore_errors=True)
|
||
os.mkdir(output_dir)
|
||
master_element_tree = ET.ElementTree(
|
||
ET.fromstring('<corpus>\n</corpus>')
|
||
)
|
||
for corpus_file in self.files:
|
||
corpus_file_path = os.path.join(corpus_dir, corpus_file.filename)
|
||
element_tree = ET.parse(corpus_file_path)
|
||
text_node = element_tree.find('text')
|
||
text_node.set('address', corpus_file.address or "NULL")
|
||
text_node.set('author', corpus_file.author)
|
||
text_node.set('booktitle', corpus_file.booktitle or "NULL")
|
||
text_node.set('chapter', corpus_file.chapter or "NULL")
|
||
text_node.set('editor', corpus_file.editor or "NULL")
|
||
text_node.set('institution', corpus_file.institution or "NULL")
|
||
text_node.set('journal', corpus_file.journal or "NULL")
|
||
text_node.set('pages', corpus_file.pages or "NULL")
|
||
text_node.set('publisher', corpus_file.publisher or "NULL")
|
||
text_node.set('publishing_year', str(corpus_file.publishing_year))
|
||
text_node.set('school', corpus_file.school or "NULL")
|
||
text_node.set('title', corpus_file.title)
|
||
element_tree.write(corpus_file_path)
|
||
master_element_tree.getroot().insert(1, text_node)
|
||
output_file = os.path.join(output_dir, 'corpus.vrt')
|
||
master_element_tree.write(output_file,
|
||
xml_declaration=True,
|
||
encoding='utf-8')
|
||
self.last_edited_date = datetime.utcnow()
|
||
self.status = 'submitted'
|
||
|
||
def delete(self):
|
||
corpus_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
|
||
str(self.user_id),
|
||
'corpora',
|
||
str(self.id))
|
||
shutil.rmtree(corpus_dir, ignore_errors=True)
|
||
db.session.delete(self)
|
||
|
||
def __repr__(self):
|
||
'''
|
||
String representation of the corpus. For human readability.
|
||
'''
|
||
return '<Corpus {corpus_title}>'.format(corpus_title=self.title)
|
||
|
||
|
||
class QueryResult(db.Model):
|
||
'''
|
||
Class to define a corpus analysis result.
|
||
'''
|
||
__tablename__ = 'query_results'
|
||
# Primary key
|
||
id = db.Column(db.Integer, primary_key=True)
|
||
# Foreign keys
|
||
user_id = db.Column(db.Integer, db.ForeignKey('users.id'))
|
||
# Fields
|
||
description = db.Column(db.String(255))
|
||
filename = db.Column(db.String(255))
|
||
query_metadata = db.Column(db.JSON())
|
||
title = db.Column(db.String(32))
|
||
|
||
def delete(self):
|
||
query_result_dir = os.path.join(current_app.config['NOPAQUE_STORAGE'],
|
||
str(self.user_id),
|
||
'query_results',
|
||
str(self.id))
|
||
shutil.rmtree(query_result_dir, ignore_errors=True)
|
||
db.session.delete(self)
|
||
|
||
def to_dict(self):
|
||
return {'id': self.id,
|
||
'user_id': self.user_id,
|
||
'description': self.description,
|
||
'filename': self.filename,
|
||
'query_metadata': self.query_metadata,
|
||
'title': self.title}
|
||
|
||
def __repr__(self):
|
||
'''
|
||
String representation of the CorpusAnalysisResult. For human readability.
|
||
'''
|
||
return '<QueryResult {}>'.format(self.title)
|
||
|
||
|
||
'''
|
||
' Flask-Login is told to use the application’s custom anonymous user by setting
|
||
' its class in the login_manager.anonymous_user attribute.
|
||
'''
|
||
login_manager.anonymous_user = AnonymousUser
|
||
|
||
|
||
@login_manager.user_loader
|
||
def load_user(user_id):
|
||
return User.query.get(int(user_id))
|