Remove `bin/genenetwork2` Script

Description

The `bin/genenetwork2` script was used for a really long time to launch Genenetwork2, and has served that purpose with honour and dedication. We applaud that.

It is, however, time to retire the script, since at this point in time, it serves more to obfuscate the startup that as a helpful tool.

On production, we have all but abandoned the use of the script, and we need to do the same for CI/CD, and eventually, development.

This issue tracks the process, and problems that come up during the move to retire the script.

Process

[x] Identify how to run unit tests without the script
[x] Document how to run unit tests without the script
[x] Identify how to run mechanical-rob tests without the script
[x] Document how to run mechanical-rob tests without the script
[ ] Update CI/CD definitions to get rid of the references to the script
[ ] Delete the script from the repository

Setup

First, we need to setup the following mandatory environment variables:

GN2_PROFILE
GN2_SETTINGS
JS_GUIX_PATH
GEMMA_COMMAND
PLINK_COMMAND
GEMMA_WRAPPER_COMMAND
REQUESTS_CA_BUNDLE

Within a guix shell, you could do that with something like:

export GN2_PROFILE="${GUIX_ENVIRONMENT}"
export GN2_SETTINGS="/home/frederick/genenetwork/gn2_settings.conf"
export JS_GUIX_PATH="${GN2_PROFILE}/share/genenetwork2/javascript"
export GEMMA_COMMAND="${GN2_PROFILE}/bin/gemma"
export PLINK_COMMAND="${GN2_PROFILE}/bin/plink2"
export GEMMA_WRAPPER_COMMAND="${GN2_PROFILE}/bin/gemma-wrapper"
export REQUESTS_CA_BUNDLE="${GUIX_ENVIRONMENT}/etc/ssl/certs/ca-certificates.crt"

Note that, you can define all the variables derived from "GN2_PROFILE" in your settings file, if such a settings file is computed.

Running Unit Tests

To run unit tests, run pytest at the root of the repository.

$ cd /path/to/genenetwork2
$ pytest

Running "mechanical-rob" Tests

At the root of the repository, run something like:

python test/requests/test-website.py --all http://localhost:5033

Change the port, as appropriate.

Launching Application

In addition to the minimum set of envvars defined in the "Setup" section above, we need the following variables defined to get the application to launch:

FLASK_APP

In a guix shell, you could do:

export FLASK_APP="gn2.wsgi"

Now you can launch the application with flask with something like:

flask run --port=5033 --with-threads

or with green unicorn with something like:

gunicorn --reload \
         --workers 3 \
         --timeout 1200 \
         --log-level="debug" \
         --keep-alive 6000 \
         --max-requests 10 \
         --bind="127.0.0.1:5033" \
         --max-requests-jitter 5 \
         gn2.wsgi:application

You can change the gunicorn setting to fit your scenario.