Source code for bio2bel.manager.flask_manager

# -*- coding: utf-8 -*-

"""Provides abstractions over the management of SQLAlchemy connections and sessions."""

import os
import sys
from typing import List, Optional, Union

import click
from sqlalchemy.ext.declarative import DeclarativeMeta

from .cli_manager import CliMixin
from .connection_manager import ConnectionManager
from ..exc import Bio2BELMissingModelsError

__all__ = [

[docs]class FlaskMixin(ConnectionManager, CliMixin): """A mixin for building a Flask-Admin interface. This class can be used as a mixin, meaning that a class inheriting from AbstractManager can also multiple-inherit from this class. It contains functions to build a :mod:`flask` application for easy viewing of the contents of the database. First, you'll have to make sure that the :mod:`flask` and :mod:`flask-admin` are installed. They can be installed with Bio2BEL using the package extra called "web" like: .. code-block:: bash $ pip install bio2bel[web] Or, installed directly with `pip`: .. code-block:: bash $ pip install flask flask-admin Besides this, all that's necessary to use this mixin is to define the class variable ``flask_admin_models`` as a list of SQLAlchemy models you'd like to see. .. code-block:: python >>> from sqlalchemy.ext.declarative import DeclarativeMeta >>> >>> from bio2bel import AbstractManager >>> from bio2bel.manager.flask_manager.FlaskMixin >>> >>> from .constants import MODULE_NAME >>> from .models import Base, Evidence, Interaction, Mirna, Species, Target >>> >>> class Manager(AbstractManager): ... module_name = MODULE_NAME ... flask_admin_models = [Evidence, Interaction, Mirna, Species, Target] ... ... @property ... def _base(self) -> DeclarativeMeta: ... return Base ... ... def populate(self) -> None: ... ... """ #: Represents a list of SQLAlchemy classes to make a Flask-Admin interface. flask_admin_models: Union[DeclarativeMeta, List[DeclarativeMeta]] def __init__(self, *args, **kwargs): # noqa: D107 if not hasattr(self, 'flask_admin_models') or not self.flask_admin_models: raise Bio2BELMissingModelsError('FlaskMixin requires the class variable "flask_admin_models".') super().__init__(*args, **kwargs) def _add_admin(self, app, **kwargs): """Add a Flask Admin interface to an application. :param flask.Flask app: A Flask application :param kwargs: Keyword arguments are passed through to :class:`flask_admin.Admin` :rtype: flask_admin.Admin """ from flask_admin import Admin from flask_admin.contrib.sqla import ModelView admin = Admin(app, **kwargs) for flask_admin_model in self.flask_admin_models: if isinstance(flask_admin_model, tuple): # assume its a 2 tuple if len(flask_admin_model) != 2: raise TypeError model, view = flask_admin_model admin.add_view(view(model, self.session)) else: admin.add_view(ModelView(flask_admin_model, self.session)) return admin
[docs] def get_flask_admin_app(self, url: Optional[str] = None, secret_key: Optional[str] = None): """Create a Flask application. :param url: Optional mount point of the admin application. Defaults to ``'/'``. :rtype: flask.Flask """ from flask import Flask app = Flask(__name__) if secret_key: app.secret_key = secret_key self._add_admin(app, url=(url or '/')) return app
@staticmethod def _cli_add_flask(main: click.Group) -> click.Group: """Add the web command.""" return add_cli_flask(main)
[docs] @classmethod def get_cli(cls) -> click.Group: """Add a :mod:`click` main function to use as a command line interface.""" main = super().get_cli() cls._cli_add_flask(main) return main
def add_cli_flask(main: click.Group) -> click.Group: # noqa: D202 """Add a ``web`` comand main :mod:`click` function.""" @main.command() @click.option('-v', '--debug', is_flag=True) @click.option('-p', '--port') @click.option('-h', '--host') @click.option('-k', '--secret-key', default=os.urandom(8)) @click.pass_obj def web(manager, debug, port, host, secret_key): """Run the web app.""" if not manager.is_populated(): click.echo(f'{manager.module_name} has not yet been populated') sys.exit(0) app = manager.get_flask_admin_app(url='/', secret_key=secret_key), host=host, port=port) return main