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

Category: Biosphere
Sub Category: Terrestrial Wildlife

Keywords from Contributors

measur transforms archiving animals conversion observation optimize projection compose generic

Last synced: about 4 hours ago
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Repository metadata

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 (over 7 years ago)
• Default Branch: master
• Last Pushed: 2025-04-22T01:17:14.000Z (9 days ago)
• Last Synced: 2025-04-25T13:48:16.793Z (5 days ago)
• Language: Python
• Homepage: https://tsx.org.au
• Size: 53.1 MB
• Stars: 6
• Watchers: 1
• Forks: 1
• Open Issues: 3
• Releases: 0
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

README.rst

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

        

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Owner metadata

• Name: NESP Threatened Species Recovery Hub (Project 3.1)
• Login: nesp-tsr3-1
• Email:
• Kind: organization
• Description:
• Website:
• Location:
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/33853157?v=4
• Repositories: 1
• Last ynced at: 2023-03-08T18:46:30.031Z
• Profile URL: https://github.com/nesp-tsr3-1

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GitHub Events

Total

• Push event: 35
• Pull request event: 1
• Create event: 1

Last Year

• Push event: 35
• Pull request event: 1
• Create event: 1

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Committers metadata

Last synced: 1 day ago

Name	Email	Commits
James Watmuff	j****s@p****u	744
James Watmuff	j****s@J****l	144
James Watmuff	j****s@J****y	54
hoangnguyen177	h****7@g****m	23
Ubuntu	u****u@n****u	8
Ubuntu	u****u@n****u	2
dependabot[bot]	4****]	1

Committer domains:

• nesp-dev.coesra.org.au: 1
• nesp-dev1.coesra.org.au: 1
• jamess-mbp.home.gateway: 1
• planticle.com.au: 1

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Issue and Pull Request metadata

Last synced: 1 day ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/nesp-tsr3-1/tsx

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Dependencies

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