https://github.com/nesp-tsr3-1/tsx

Australian Threatened Species Index
https://github.com/nesp-tsr3-1/tsx

Last synced: about 2 months ago
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Australian Threatened Species Index

• Host: GitHub
• URL: https://github.com/nesp-tsr3-1/tsx
• Owner: nesp-tsr3-1
• License: mit
• Created: 2017-11-21T03:30:08.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2024-03-22T00:37:20.000Z (10 months ago)
• Last Synced: 2024-03-23T07:06:12.274Z (10 months ago)
• Language: Python
• Homepage: https://tsx.org.au
• Size: 8.37 MB
• Stars: 5
• Watchers: 2
• Forks: 1
• Open Issues: 11
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

• open-sustainable-technology - TSX - Provides reliable and robust measures of change in the relative abundance of Australia's threatened and near-threatened species at national, state and regional levels. (Biosphere / Terrestrial Wildlife)

README

        
===================================================================

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:

.. code:: bash

	mysql tsx < data/sql/create.sql

	mysql tsx < data/sql/init.sql

Copy example configuration:

.. code:: bash

	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

------------------------------------------------------------

.. code:: bash

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

	pipenv sync

3. Import taxa

--------------

.. code:: bash

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

4. Import some sample data

--------------------------

Via command line:

.. code:: bash

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

Or alternatively via web upload interface

.. code:: bash

	# 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

-------------------------

.. code:: bash

	python -m tsx.process alpha_hull

	python -m tsx.process range_ultrataxon

	python -m tsx.process pseudo_absence

Or all at once:

.. code:: bash

	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