class Interface(db.Model):
"""
represents an interface a biobox or task can implement.
"""
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String, unique=True, nullable=False)
tasks = db.relationship('Task', backref='interface', lazy='dynamic')
class Role(db.Model):
"""
roles a user can assume.
admin, trusted, common and base
"""
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String, unique=True, nullable=False)
description = db.Column(db.String)
class Source(db.Model):
"""
represents a source from where bioboxes are loaded.
"""
id = db.Column(db.Integer, primary_key=True)
url = db.Column(db.String, unique=True, nullable=False)
name = db.Column(db.String, unique=True, nullable=False)
bioboxes = db.relationship('Biobox',
cascade='all, delete-orphan',
backref='source',
lazy='dynamic')
class Task(db.Model):
"""
represents the tasks a biobox can perform.
"""
KEY_NAME = 'name'
KEY_INTERFACE = 'interface'
id = db.Column(db.Integer, primary_key=True)
name = db.Column(db.String, nullable=False)
interface_id = db.Column(db.Integer,
db.ForeignKey('interface.id'),
nullable=False)
class Image(db.Model):
"""
represents the image part of a biobox.
existence is based solely on the quest for conformity with the schema.
"""
KEY_CONTAINER_URI = 'dockerhub'
KEY_REPO_URL = 'repo'
KEY_SRC_URL = 'source'
id = db.Column(db.Integer, primary_key=True)
dockerhub = db.Column(db.String, unique=True, nullable=False)
repo = db.Column(db.String, unique=True, nullable=False)
source = db.Column(db.String)
biobox_id = db.Column(db.Integer,
db.ForeignKey("biobox.pmid"),
nullable=False)
biobox = db.relationship("Biobox", back_populates='image', uselist=False)
class Biobox(db.Model):
"""
represents a standard biobox.
"""
KEY_IMAGE = 'image'
KEY_ID = 'pmid'
KEY_HOME_PAGE = 'homepage'
KEY_MAILING_LIST = 'mailing_list'
KEY_DESCRIPTION = 'description'
KEY_TASKS = 'tasks'
KEY_TITLE = 'title'
pmid = db.Column(db.Integer, primary_key=True)
title = db.Column(db.String, unique=True, nullable=False)
homepage = db.Column(db.String)
mailing_list = db.Column(db.String)
description = db.Column(db.String, nullable=False)
tasks = db.relationship('Task', cascade='all', secondary=biobox_tasks)
image = db.relationship('Image',
cascade='all',
uselist=False,
back_populates='biobox')
source_id = db.Column(db.Integer,
db.ForeignKey('source.id'),
nullable=False)
class User(db.Model):
"""
user representation
"""
id = db.Column(db.Integer, primary_key=True)
username = db.Column(db.String, unique=True, nullable=False)
email = db.Column(db.String, unique=True, nullable=False)
password_hash = db.Column(db.String, nullable=False)
active = db.Column(db.Boolean())
confirmed_at = db.Column(db.DateTime())
roles = db.relationship('Role',
secondary=roles_users,
backref=db.backref('users', lazy='dynamic'))
def hash_password(self, password):
"""
creates a password hash.
"""
self.password_hash = pwd_context.encrypt(password)
def verify_password(self, password):
"""
verifies the password of the user.
"""
return pwd_context.verify(password, self.password_hash)
def generate_auth_token(self, expiration=600):
"""
generates a new authentication token for the user.
"""
s = Serializer(SECRET_KEY, expires_in=expiration)
return s.dumps({'id': self.id})
@staticmethod
def verify_auth_token(token):
"""
verifies the authentication token of the user.
"""
s = Serializer(SECRET_KEY)
data = s.loads(token)
user = User.query.get(data['id'])
return user
import json
import os.path
import requests
import yaml
from itsdangerous import (TimedJSONWebSignatureSerializer as Serializer)
from jsonschema import validate
from passlib.apps import custom_app_context as pwd_context
from bioboxgui import db
from config import basedir, SECRET_KEY
# linking bioboxes with tasks since 2016.
biobox_tasks = db.Table(
'association', db.Model.metadata,
db.Column('biobox_id', db.Integer, db.ForeignKey('biobox.pmid')),
db.Column('task_id', db.Integer, db.ForeignKey('task.id')))
# many to many relationship between users and roles.
roles_users = db.Table(
'roles_users', db.Column('user_id', db.Integer, db.ForeignKey('user.id')),
db.Column('role_id', db.Integer, db.ForeignKey('role.id')))
class Role(db.Model):
"""
roles a user can assume.
admin, trusted, common and base
"""