Welcome to the Australian Threatened Species Index (TSX) Repository

For information about the Australian Threatened Species Index project, see https://tsx.org.au

The code in this repository is responsible for data import and pre-processing of data, and visualsation of the generated trend graphs and associated data.

User Guide

The easiest way to learn about running the TSX workflow is to check out the User Guide at https://tsx.org.au/user-guide/

Developer Guide

1. Setup database (MySQL)

First create a new MySQL database.

You can call it anything but the instructions below assume it is named "tsx".

Initialise the database using the provided scripts:

mysql tsx < data/sql/create.sql
mysql tsx < data/sql/init.sql

Copy example configuration:

cp tsx.conf.example tsx.conf

Then edit the [database] section in tsx.conf to match the database you just created.

2. Setup python virtual environment and install dependencies

pip install pipenv # if you don't have virtualenv already
pipenv sync

3. Import taxa

python -m tsx.import_taxa [path to TaxonList.xlsx]

4. Import some sample data

Via command line:

python -m tsx.importer --type 1 --commit data/type-1-sample.csv

Or alternatively via web upload interface

# Start back-end API:
FLASK_DEBUG=1 FLASK_APP=tsx/api/api.py python -m flask run

# Start front-end (in a separate terminal):
cd web
npm install
npm run dev-data

5. Run processing scripts

python -m tsx.process alpha_hull
python -m tsx.process range_ultrataxon
python -m tsx.process pseudo_absence

Or all at once:

python -m tsx.process -c all

Deployment

(TODO - more detailed instructions)

1. Setup database (see instructions for dev environment)

2. Install tsx package:

   python setup.py install
   

3. Edit configuration in /opt/tsx/conf/tsx.conf

4. Setup as service (Linux):

   sudo cp etc/init.d/tsxapi /etc/init.d/
   sudo service tsxapi start
   

5. Deploy static resources:

   # If you don't have have node/npm installed:
   #
   # sudo apt install npm nodejs
   #
   # .. or might need a more recent version ..
   #
   # sudo apt-get remove nodejs npm ## remove existing nodejs and npm packages
   # sudo apt-get install curl
   # curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
   # sudo apt-get install -y nodejs
   #
   
   cd web
   npm install
   (TODO - add step to point code to REST API base URL)
   npm run build
   sudo cp -r dist/ /var/www/tsx/
   sudo chown -R www-data:www-data /var/www/tsx