# Justice 40 Score application

<details open="open">
<summary>Table of Contents</summary>

<!-- TOC -->

- [About this application](#about-this-application)
  - [Score comparison workflow](#score-comparison-workflow)
    - [Workflow Diagram](#workflow-diagram)
    - [Step 0: Set up your environment](#step-0-set-up-your-environment)
    - [Step 1: Run the ETL script for each data source](#step-1-run-the-etl-script-for-each-data-source)
    - [Step 2: Calculate the Justice40 score experiments](#step-2-calculate-the-justice40-score-experiments)
    - [Step 3: Compare the Justice40 score experiments to other indices](#step-3-compare-the-justice40-score-experiments-to-other-indices)
  - [Data Sources](#data-sources)
- [Running using Docker](#running-using-docker)
- [Log visualization](#log-visualization)
- [Local development](#local-development)
  - [Downloading Census Block Groups GeoJSON and Generating CBG CSVs](#downloading-census-block-groups-geojson-and-generating-cbg-csvs)
  - [Generating mbtiles](#generating-mbtiles)
  - [Serve the map locally](#serve-the-map-locally)
  - [Running Jupyter notebooks](#running-jupyter-notebooks)
  - [Activating variable-enabled Markdown for Jupyter notebooks](#activating-variable-enabled-markdown-for-jupyter-notebooks)
- [Miscellaneous](#miscellaneous)

<!-- /TOC -->

</details>

## About this application

This application is used to compare experimental versions of the Justice40 score to established environmental justice indices, such as EJSCREEN, CalEnviroScreen, and so on.

_**NOTE:** These scores **do not** represent final versions of the Justice40 scores and are merely used for comparative purposes. As a result, the specific input columns and formulas used to calculate them are likely to change over time._


### Score comparison workflow

The descriptions below provide a more detailed outline of what happens at each step of ETL and score calculation workflow.

#### Workflow Diagram

TODO add mermaid diagram

#### Step 0: Set up your environment

1. After cloning the project locally, change to this directory: `cd score`
1. Choose whether you'd like to run this application using Docker or if you'd like to install the dependencies locally so you can contribute to the project.
    - **With Docker:** Follow these [installation instructions](https://docs.docker.com/get-docker/) and skip down to the [Running with Docker section](#running-with-docker) for more information
    - **For Local Development:** Skip down to the [Local Development section](#local-development) for more detailed installation instructions


#### Step 1: Run the ETL script for each data source

1. Call the `etl-run` command using the application manager `application.py` **NOTE:** This may take several minutes to execute.
   - With Docker: `docker run --rm -it j40_score /bin/sh -c "python3 application.py etl-run"`
   - With Poetry: `poetry run python application.py etl-run`
1. The `etl-run` command will execute the corresponding ETL script for each data source in `etl/sources/`. For example, `etl/sources/ejscreen/etl.py` is the ETL script for EJSCREEN data.
1. Each ETL script will extract the data from its original source, then format the data into `.csv` files that get stored in the relevant folder in `data/dataset/`. For example, HUD Housing data is stored in `data/dataset/hud_housing/usa.csv`

_**NOTE:** You have the option to pass the name of a specific data source to the `etl-run` command, which will limit the execution of the ETL process to that specific data source._
_For example: `poetry run python application.py etl-run ejscreen` would only run the ETL process for EJSCREEN data._

#### Step 2: Calculate the Justice40 score experiments

1. Call the `score-run` command using the application manager `application.py` **NOTE:** This may take several minutes to execute.
   - With Docker: `docker run --rm -it j40_score /bin/sh -c "python3 application.py score-run"`
   - With Poetry: `poetry run python application.py score-run`
1. The `score-run` command will execute the `etl/score/etl.py` script which loads the data from each of the source files added to the `data/dataset/` directory by the ETL scripts in Step 1.
1. These data sets are merged into a single dataframe using their Census Block Group GEOID as a common key, and the data in each of the columns is standardized in two ways:
    - Their [percentile rank](https://en.wikipedia.org/wiki/Percentile_rank) is calculated, which tells us what percentage of other Census Block Groups have a lower value for that particular column.
    - They are normalized using [min-max normalization](https://en.wikipedia.org/wiki/Feature_scaling), which adjusts the scale of the data so that the Census Block Group with the highest value for that column is set to 1, the Census Block Group with the lowest value is set to 0, and all of the other values are adjusted to fit within that range based on how close they were to the highest or lowest value.
1. The standardized columns are then used to calculate each of the Justice40 score experiments described in greater detail below, and the results are exported to a `.csv` file in [`data/score/csv`](data/score/csv)

#### Step 3: Compare the Justice40 score experiments to other indices

1. TODO: Describe the steps for this

### Data Sources

- **[EJSCREEN](etl/sources/ejscreen):** TODO Add description of data source
- **[Census](etl/sources/census):** TODO Add description of data source
- **[American Communities Survey](etl/sources/census_acs):** TODO Add description of data source
- **[Housing and Transportation](etl/sources/housing_and_transportation):** TODO Add description of data source
- **[HUD Housing](etl/sources/hud_housing):** TODO Add description of data source
- **[HUD Recap](etl/sources/hud_recap):** TODO Add description of data source
- **[CalEnviroScreen](etl/scores/calenviroscreen):** TODO Add description of data source


## Running using Docker

We use Docker to install the necessary libraries in a container that can be run in any operating system.

To build the docker container the first time, make sure you're in the root directory of the repository and run `docker-compose build`.

Once completed, run `docker-compose up` and then open a new tab or terminal window, and then run any command for the application using this format:
`docker exec j40_data_pipeline_1 python3 application.py [command]`

Here's a list of commands:

- Get help: `docker exec j40_data_pipeline_1 python3 application.py --help"`
- Clean up the census data directories: `docker exec j40_data_pipeline_1 python3 application.py census-cleanup"`
- Clean up the data directories: `docker exec j40_data_pipeline_1 python3 application.py data-cleanup"`
- Generate census data: `docker exec j40_data_pipeline_1 python3 application.py census-data-download"`
- Run all ETL processes: `docker exec j40_data_pipeline_1 python3 application.py etl-run"`
- Generate Score: `docker exec j40_data_pipeline_1 python3 application.py score-run"`

## Local development

You can run the Python code locally without Docker to develop, using Poetry. However, to generate the census data you will need the [GDAL library](https://github.com/OSGeo/gdal) installed locally. Also to generate tiles for a local map, you will need [Mapbox tippeanoe](https://github.com/mapbox/tippecanoe). Please refer to the repos for specific instructions for your OS.

### Windows Users
- If you want to download Census data or run tile generation, please install TippeCanoe [following these instrcutions](https://github.com/GISupportICRC/ArcGIS2Mapbox#installing-tippecanoe-on-windows).
- If you want to generate tiles, you need some pre-requisites for Geopandas as specified in the Poetry requirements. Please follow [these instructions](https://stackoverflow.com/questions/56958421/pip-install-geopandas-on-windows) to install the Geopandas dependency locally.

### Setting up Poetry

- Start a terminal
- Change to this directory (`/data/data-pipeline`)
- Make sure you have Python 3.9 installed: `python -V` or `python3 -V`
- We use [Poetry](https://python-poetry.org/) for managing dependencies and building the application. Please follow the instructions on their site to download.
- Install Poetry requirements with `poetry install`

### Downloading Census Block Groups GeoJSON and Generating CBG CSVs

- Make sure you have Docker running in your machine
- Start a terminal
- Change to this directory (i.e. `cd data/data-pipeline`)
- If you want to clear out all data and tiles from all directories, you can run: `poetry run python application.py data-cleanup`.
- Then run `poetry run python application.py census-data-download`
  Note: Census files are not kept in the repository and the download directories are ignored by Git

### Generating mbtiles

- TBD

### Serve the map locally

- Start a terminal
- Change to this directory (i.e. `cd data/data-pipeline`)
- Run: `docker run --rm -it -v ${PWD}/data/tiles:/data -p 8080:80 maptiler/tileserver-gl`

### Running Jupyter notebooks

- Start a terminal
- Change to this directory (i.e. `cd data/data-pipeline`)
- Run `poetry run jupyter notebook`. Your browser should open with a Jupyter Notebook tab

### Activating variable-enabled Markdown for Jupyter notebooks

- Change to this directory (i.e. `cd data/data-pipeline`)
- Activate a Poetry Shell (see above)
- Run `jupyter contrib nbextension install --user`
- Run `jupyter nbextension enable python-markdown/main`
- Make sure you've loaded the Jupyter notebook in a "Trusted" state. (See button near
  top right of Notebook screen.)

For more information, see [nbextensions docs](https://jupyter-contrib-nbextensions.readthedocs.io/en/latest/install.html) and
see [python-markdown docs](https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tree/master/src/jupyter_contrib_nbextensions/nbextensions/python-markdown).

## Miscellaneous

- To export packages from Poetry to `requirements.txt` run `poetry export --without-hashes > requirements.txt`