# genenetwork3 GeneNetwork3 REST API for data science and machine learning ## Installation #### Using guix Simply load up the environment (for development purposes): ```bash guix environment --load=guix.scm ``` Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up. ```bash env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm python3 import redis ``` Better run a proper container ``` env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm ``` If you get a Guix error, such as `ice-9/boot-9.scm:1669:16: In procedure raise-exception: error: python-sqlalchemy-stubs: unbound variable` it typically means an update to guix latest is required (i.e., guix pull): ``` guix pull source ~/.config/guix/current/etc/profile ``` and try again. See also instructions in [.guix.scm](.guix.scm). #### Using a Guix profile (or rolling back) Create a new profile with ``` env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix package -i genenetwork3 -p ~/opt/genenetwork3 ``` and load the profile settings with ``` source ~/opt/genenetwork3/etc/profile start server... ``` Note that GN2 profiles include the GN3 profile (!). To roll genenetwork3 back you can use either in the same fashion (probably best to start a new shell first) ``` bash source ~/opt/genenetwork2-older-version/etc/profile set|grep store run tests, server etc... ``` #### Running Tests (assuming you are in a guix container; otherwise use venv!) To run tests: ```bash python -m unittest discover -v ``` Running pylint: ```bash pylint *py tests gn3 ``` Running mypy(type-checker): ```bash mypy . ``` #### Running the flask app To spin up the server on its own (for development): ```bash env FLASK_DEBUG=1 FLASK_APP="main.py" flask run --port=8080 ``` And test with ``` curl localhost:8080/api/version "1.0" ``` To run with gunicorn ``` gunicorn --bind 0.0.0.0:8080 wsgi:app ``` consider the following options for development `--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi`. And for the scalable production version run ``` gunicorn --bind 0.0.0.0:8080 --workers 8 --keep-alive 6000 --max-requests 10 --max-requests-jitter 5 --timeout 1200 wsgi:app ``` ##### Using python-pip IMPORTANT NOTE: we do not recommend using pip tools, use Guix instead 1. Prepare your system. You need to make you have python > 3.8, and the ability to install modules. 2. Create and enter your virtualenv: ```bash virtualenv --python python3 venv . venv/bin/activate ``` 3. Install the required packages ```bash # The --ignore-installed flag forces packages to # get installed in the venv even if they existed # in the global env pip install -r requirements.txt --ignore-installed ``` #### A note on dependencies Make sure that the dependencies in the `requirements.txt` file match those in guix. To freeze dependencies: ```bash # Consistent way to ensure you don't capture globally # installed packages pip freeze --path venv/lib/python3.8/site-packages > requirements.txt ```