Syncronise NOFA taxon list with GBIF / Artsdatabanken

[ninsbl]

Taxon list (nofa."l_taxon") in NOFA should be synchronized with taxonomic backbone at Artsdatabanken / GBIF. See also:

5

and https://github.com/NINAnor/invafish/blob/master/nofa/fix_taxon.sh

[andersfi]

Preliminary script (R) for autoresolving added to NINAnor/invafish/nofa as https://github.com/NINAnor/invafish/blob/master/nofa/l_taxon_autoresolve.R and https://github.com/NINAnor/invafish/blob/master/nofa/function_scientific_name_lookup.R . Should be revised, and finally merged into https://github.com/NINAnor/invafish/blob/master/nofa/fix_taxon.sh .

Also, comments to l_taxon table indicating e.g. which columns are auto-resolved added to https://github.com/NINAnor/invafish/blob/master/nofa/l_taxon_comments.sql

[ninsbl]

Cool! I will fix that tomorrow!

[andersfi]

Updated R script for automatically resolve taxon information and storing back into l_taxon (https://github.com/NINAnor/invafish/blob/master/update_l_taxon/l_taxon_autoresolve.R). Keeping the issue/improvement open for now, as the script should be revised slightly if run as cronjob. Is not tested thoroughly, particularly need to resolve issues around the stability of taxonIDs from artsnavnabasen.