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 = ...
- Install python dependencies (requires
conda to be installed):
conda env create -f environment.yml
conda activate export-taxa-table
- 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. - 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"
...