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Taxa Tree Generator (Catalogue of Life)

This website generates a taxa tree compatible with Workbench and Wizzard from Specify 6 and Specify 7.

Data credit

The data used by this tool comes from Catalogue of Life Dataset.

Citation:

Bánki, O., Roskov, Y., Vandepitte, L., DeWalt, R. E., Remsen, D., Schalk, P., Orrell, T., Keping, M., Miller, J., Aalbu, R., Adlard, R., Adriaenssens, E., Aedo, C., Aescht, E., Akkari, N., Alonso-Zarazaga, M. A., Alvarez, B., Alvarez, F., Anderson, G., et al. (2021). Catalogue of Life Checklist (Version 2021-09-21). Catalogue of Life. https://doi.org/10.48580/d4sv

Requirements

Back-end

Python 3.6+

Dependencies are specified in requirements.txt

# Create a virtual environment
python -m venv venv

# Install dependencies
venv/bin/pip install -r requirements.txt

Front-end

  1. PHP 7.2+ (older versions may work)
  2. PHP Zip
  3. Any Webserver

Installation

All of the configuration parameters you must change for the site to work are located in ./front_end/config/required.php Optional parameters are located in ./front_end/config/optional.php

  1. Open the ./front_end/config/required.php file. Change the logic to properly detect correct CONFIGURATION and DEVELOPMENT constant values. The value of DEVELOPMENT will affect the error reporting level.
  2. Set LINK to an address the website would be served on.
  3. Set WORKING_LOCATION to an empty folder. This would be the destination for all the files created in the process. Make sure the webserver and the user that would execute back_end/refresh_data.py has READ and WRITE permissions to this folder. Warning! Files present in this directory may be deleted.
  4. Run back_end/refresh_data.py. This will automatically check for new versions of the taxa tree and download it. You should also setup a daily or monthly CRON job for this file to keep your data up to date
  5. Configure your webserver to point to front_end directory.

Optional settings

You can go over the other settings in the ./front_end/config/optional.php file and see if there is anything you would like to adjust.

For example:

  1. You can configure stats reporting by making STATS_URL point to a location of collect/ script from Taxa Tree Stats reporter

Credit for used resources

There were snippets of code/files from the following resources used: