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Arboverse

Arboviruses geographic info

Quick setup

Note: when running commands in docker, your .env needs to have the PGSQL host as db. When running code from the terminal here, you need the .env to reflect the host as localhost.

Running for the First Time

  1. Clone this project
  2. Install Docker and Docker Compose
  3. Navigate to the project root.
  4. Populate the values of .env.sample to match your desired configuration, and remove .sample from the filename.
  5. Run docker-compose up --build -d.
  6. Run the command py schema_populator.py once you have verified that the db is running to build out the full database.

With that, your application should be running. You may access it at http://localhost:8000. As long as docker continues to run, this service will run in the background. When docker is restarted, the service too should be restarted automatically. If not, you can rerun the command.

Note: It may take a minute or two for the site to be accessible. A health check is performed on the database to ensure that the containers load in the correct order.

Creating a Superuser

Firstly, make sure that your env PGSQL_HOST is set to db. Then run docker-compose run --rm web python manage.py createsuperuser and follow the prompts.

Seeing the Logs

Got stuck somewhere? You can see the logs with docker-compose logs.

If you're only interested in Django's logs, run docker-compose logs web. If you're only interested in database's logs, run docker-compose logs db.

Using the Shell

Our Django setup comes with a very handy super shell. It is useful to interact with our code in a REPL shell.

Run it with docker-compose run --rm web python manage.py shell_plus

Running Tests

docker-compose run --rm web pytest

Developing Locally

  1. Create a virtual environment python -m venv env
  2. Activate it source env/bin/activate
  3. Install the requirements with pip install -r requirements/requirements.txt

Setup pre-commit

  1. Install pre-commit
  2. Run pre-commit install -t pre-commit -t pre-push
  3. Optional: you may run all hooks with pre-commit run --all

Prod Setup

Run python manage.py collectstatic and ensure that the resulting folder will be web-accessible.

Make sure to change username and password in .env and in docker-compose.yml to match your production database.

Creating a Virus Layer

The virus_geojson_builder.py contains code to generate new GeoJSON layers for displaying the presence of viruses in countries around the world. When run, the program will look for a GeoJSON folder and a shapefile which describes the countries around the world in a way that can be broken down into geometries. In my implementation, I used free maps from Natural Earth Data to source my shapefile.

The script also expects an excel document following the format of The global distribution of arbovirus diversity - OFFICIAL.xlsx included in this repo.

Once you have the resulting GeoJSON file, you can go to mapbox and upload the data as a new layer for the map. The script will have associated each virus to the ISO of each country which Mapbox can interpret to build a layer for you. From there, you can use the id to render a layer out in /arboverse_updated/static/js/mapboxutil.js.

Python Scripts

Each of these scripts have been added for a specific purpose.

  1. mapbox_api_upload.py - This script is used to upload the GeoJSON file to Mapbox and create a new layer. You will need to add your Mapbox API key to the .env file for this to work.
  2. virus_geojson_builder.py - This script is used to generate a GeoJSON file from a shapefile and excel document. You will need to add the path to the shapefile and the excel document to the file for this to work.
  3. schema_populator.py - This script is used to populate the database. The script is dependent on The global distribution of arbovirus diversity - OFFICIAL.xlsx and Arbovector_database.csv to populate. If you wish to use alternative files, their names will need to be changed in the script. The format of data cannot be changed from how it is presented in these two files or it will not work.