export-taxa-table

exports the taxa table and other relevant, associated fields from a symbiota database

This requires access to a symbiota database configured in .my.cnf in the user's home directory in the following format:

[client]
user = ...
password = ...
host = ...
database = ...

1. Install python dependencies (requires conda to be installed):
   • conda env create -f environment.yml
   • conda activate export-taxa-table
2. If you want to automatically zip the output file, which can be quite large, set zipped_output = True at the top of main() in main.py. This will leave you with a zip archive containing the csv output file.
3. Run python main.py

The output file is in the following format:

"tid","parenttid","rankname","sciname","author"
1,1,"Kingdom","Animalia","Linnaeus, 1758"
2,1,"Phylum","Arthropoda","Latreille, 1829"
4,1,"Subphylum","Hexapoda","Latreille, 1825"
4,2,"Subphylum","Hexapoda","Latreille, 1825"
...