The QHAna Plugin-Registry

This package uses Poetry >=1.2 (documentation).

Original template repository: https://github.com/buehlefs/flask-template/

VSCode

For vscode install the python extension and add the poetry venv path to the folders the python extension searches for venvs.

On linux:

{
    "python.venvFolders": [
        "~/.cache/pypoetry/virtualenvs"
    ]
}

Development

Run poetry install to install dependencies.

The flask dev server loads environment variables from .flaskenv and .env. To override any variable create a .env file. Environment variables in .env take precedence over .flaskenv. See the content of the .flaskenv file for the default environment variables.

Create dev database

poetry run flask create-db

Run the development server with

poetry run flask run

Start redis instance in docker container (if not started yet) and start worker process used for executing background tasks with

poetry run invoke start-broker
poetry run invoke worker --beat --watch

Debugging the worker with PyCharm

Create a new "Run/Debug Configuration" of the type "Python Debug Server"
Follow the instructions inside this config e.g.:
1. pip install pydevd-pycharm~=241.18034.82
2. add the following code somewhere before the lines you want to debug:
```
import pydevd_pycharm
pydevd_pycharm.settrace('localhost', port=1234, stdoutToServer=True, stderrToServer=True)
```
Start the "Python Debug Server" config
Start the worker

Environment variables

the database can be configured with SQLALCHEMY_DATABASE_URI
the broker can be configured with BROKER_URL, RESULT_BACKEND and CELERY_QUEUE
the plugin discovery process can be configured with PLUGIN_DISCOVERY_INTERVAL, PLUGIN_BATCH_SIZE, PLUGIN_PURGE_INTERVAL and PLUGIN_PURGE_AFTER
environment variables that are prefixed with QHANA_ENV_ get loaded environment into the DB without the prefix
add initial seeds and services with INITIAL_PLUGIN_SEEDS and PRECONFIGURED_SERVICES
add regex rewrite rules for urls with URL_MAP_FROM_LOCALHOST and URL_MAP_TO_LOCALHOST
The docker container includes a proxy to redirect requests to the host machine. To configure the ports that should be redirected set the environment variable LOCALHOST_PROXY_PORTS to e.g. :1234 :2345.
if it runs behind a reverse proxy, set REVERSE_PROXY_COUNT to the number of trusted reverse proxies (e.g. 1)
preconfigured UiTemplates are loaded from json files specified via UI_TEMPLATE_PATHS (: separated list of paths to files/folders)

Trying out the Template

For a list of all dependencies with their license open http://localhost:5000/licenses/.

The API:

http://localhost:5000/api/

OpenAPI Documentation:

Configured in qhana_plugin_registry/util/config/smorest_config.py.

Redoc (view only): http://localhost:5000/api/redoc
Rapidoc: http://localhost:5000/api/rapidoc
Swagger-UI: http://localhost:5000/api/swagger-ui
OpenAPI Spec (JSON): http://localhost:5000/api/api-spec.json

Debug pages:

Index: http://localhost:5000/debug/
Registered Routes: http://localhost:5000/debug/routes\ Useful for looking up which endpoint is served under a route or what routes are available.

Troubleshooting

Circular imports

To investigate the cause of a circular import you can visualize the module dependencies with the package pydeps that is included in the dependencies of this project. To use pydeps you also need to install Graphvis. Please refer to the installation instruction in the documentation of pydeps.

To create a graph of all modules use pydeps qhana_plugin_registry -o graph.svg --noshow. The graph will be saved as graph.svg. This graph can be very huge and messy.

To create a graph that is small and tidy you can render only circular dependencies with pydeps qhana_plugin_registry -o graph.svg --noshow --show-cycles.

Import error for packaging version 22.0

See https://github.com/UST-QuAntiL/qhana-plugin-registry/issues/7

What this Template contains

This template uses the following libraries to build a rest app with a database on top of flask.

Flask (documentation)
Flask-Cors (documentation)\ Used to provide cors headers.\ Can be configured or removed in qhana_plugin_registry/__init__.py.
flask-babel (documentation, babel documentation)\ Used to provide translations.\ Can be configured in qhana_plugin_registry/babel.py and babel.cfg.\ Translation files and Folders: translations (and messages.pot currently in .gitignore)
Flask-SQLAlchemy (documentation, SQLAlchemy documentation)\ ORM Mapper for many SQL databases.\ Models: qhana_plugin_registry/db/models\ Config: qhana_plugin_registry/util/config/sqlalchemy_config.py and qhana_plugin_registry/db/db.py
Flask-Migrate (documentation, Alembic documentation)\ Provides automatic migration support based on alembic.\ Migrations: migrations
flask-smorest (documentation, marshmallow documentation, apispec documentation, OpenAPI spec)\ Provides the API code and generates documentation in form of a OpenAPI specification.\ API: qhana_plugin_registry/api\ API Models: qhana_plugin_registry/api/v1_api/models\ Config: qhana_plugin_registry/util/config/smorest_config.py and qhana_plugin_registry/api/__init__.py
Flask-JWT-Extended (documentation)\ Provides authentication with JWT tokens.\ Config: qhana_plugin_registry/util/config/smorest_config.py and qhana_plugin_registry/api/jwt.py
Sphinx (documentation)\ The documentation generator.\ Config: pyproject.toml and docs/conf.py (toml config input is manually configured in conf.py)
sphinxcontrib-redoc (documantation) Renders the OpenAPI spec with redoc in sphinx html output. Config: docs/conf.py (API title is read from spec)
invoke (documentation)\ tool for scripting cli tasks in python Tasks: tasks.py

Additional files and folders:

default.nix and shell.nix\ For use with the nix ecosystem.
pyproject.toml\ Poetry package config and config for the black formatter.
.flaskenv\ Environment variables loaded by the flask command and the flask dev server.
.flake8\ Config for the flake8 linter
.editorconfig
tests\ Reserved for unit tests, this template has no unit tests.
instance (in .gitignore)
qhana_plugin_registry/templates and qhana_plugin_registry/static\ Templates and static files of the flask app
docs\ Folder containing a sphinx documentation
typings\ Python typing stubs for libraries that have no type information. Mostly generated with the pylance extension of vscode.
tasks.py\ Tasks that can be executed with invoke (see invoke tasks)

Library alternatives or recommendations:

Rest API: flask-restx (documentation)
For including single page applications: flask-static-digest (documentation)
For scripting tasks: invoke (documentation)
For hashing passwords: flask-bcrypt (documentation)
For Background Task Scheduling: Celery (See also Integrating Celery with Flask)

Poetry Commands

# install dependencies from lock file in a virtualenv
poetry install

# open a shell in the virtualenv
poetry shell

# update dependencies
poetry update
poetry run invoke update-dependencies # to update other dependencies in the repository

# run a command in the virtualenv (replace cmd with the command to run without quotes)
poetry run cmd

Invoke Tasks

Invoke is a python tool for scripting cli commands. It allows to define complex commands in simple python functions in the tasks.py file.

:warning: Make sure to update the module name in tasks.py after renaming the qhana_plugin_registry module!

# list available commands
poetry run invoke --list

# update dependencies (requirements.txt in ./docs and licenses template)
poetry run invoke update-dependencies

# Compile the documentation
poetry run invoke doc

# Open the documentation in the default browser
poetry run invoke browse-doc

Babel

# initial
poetry run pybabel extract -F babel.cfg -o messages.pot .
# create language
poetry run pybabel init -i messages.pot -d translations -l en
# compile translations to be used
poetry run pybabel compile -d translations
# extract updated strings
poetry run pybabel update -i messages.pot -d translations

SQLAlchemy

# create dev db (this will NOT run migrations!)
poetry run flask create-db
# drop dev db
poetry run flask drop-db

Migrations

# create a new migration after changes in the db (Always manually review the created migration!)
poetry run flask db migrate -m "Initial migration."
# upgrade db to the newest migration
poetry run flask db upgrade
# help
poetry run flask db --help

Compiling the Documentation

# compile documentation
poetry run invoke doc

# Open the documentation in the default browser
poetry run invoke browse-doc

# Find reference targets defined in the documentation
poetry run invoke doc-index --filter=searchtext

# export/update requirements.txt from poetry dependencies (for readthedocs build)
poetry run invoke update-dependencies

Update the python source documentation

poetry run sphinx-apidoc --separate --force -o docs/source . ./tasks.py docs plugins migrations
rm docs/source/modules.rst  # delete modules file as this repository only contains one module

Acknowledgements

Current development is supported by the Federal Ministry for Economic Affairs and Energy as part of the PlanQK project (01MK20005N).

Haftungsausschluss

Dies ist ein Forschungsprototyp. Die Haftung für entgangenen Gewinn, Produktionsausfall, Betriebsunterbrechung, entgangene Nutzungen, Verlust von Daten und Informationen, Finanzierungsaufwendungen sowie sonstige Vermögens- und Folgeschäden ist, außer in Fällen von grober Fahrlässigkeit, Vorsatz und Personenschäden, ausgeschlossen.

Disclaimer of Warranty

Unless required by applicable law or agreed to in writing, Licensor provides the Work (and each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including, without limitation, any warranties or conditions of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are solely responsible for determining the appropriateness of using or redistributing the Work and assume any risks associated with Your exercise of permissions under this License.

UST-QuAntiL / qhana-plugin-registry

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