nowdatabase/documentation/functionality/species_taxonomy_checks.md

Species taxonomy checks

NOTE: This document might be outdated, especially the order/content of the lists.git

If you are unsure how the taxonomic conventions work or what the different taxonomic fields mean, you should read this document first. (NOTE: some information might be incorrect, outdated or not implemented in the new version of the app. Once an updated document is made, it should be linked here.)

In edit views which have the need for a taxonomy check, the taxonomy prop should be given to the WriteButton component. The WriteButton then runs the taxonomy checks once pressed. For example, if the user is creating a new species or editing an existing one, clicking the write button calls the functions inside taxonomyUtilities.tsx in the following order:

1. The convertTaxonomyFields function formats the taxonomy values given by the user. Everything except species_name and unique_identifier begins with a capital letter, with all other letters lowercased. The exceptions to this are special values: "incertae sedis", "indet.", "fam.", "gen." and "sp.", which are left unchanged. species_name is fully lowercased, and unique_identifier is also left unchanged.
2. The checkTaxonomy function ensures that the species does not already exist in the database, and that the taxonomy tree is correct. The function loops through every species in the database and for each one:
   1. checks that the new species is not a duplicate of an existing one (Genus, Species, an Unique identifier cannot all be identical)
   2. checks that the new species is not a synonym of an existing species
   3. checks that the (Genus, Species) pair of the new species is not identical to a (Genus, Unique Identifier) pair of an existing species
   4. checks that the taxonomy tree is correct. This is done by comparing every taxonomic field to their parent field, e.g. if the new species and the existing species have the same Family but different Order, the taxonomy tree is not valid. This has some additional rules depending on whether a taxonomic field has a special value ("incertae sedis", "indet." etc.).

If any of these checks fail, the creating/updating fails and the user is notified about it.

The taxonomyUtilities file has a bunch of functions named checkXY which check the validity of taxonomic data between fields X and Y (step 4 in the list above). For example, X could be family and Y could be subfamily, and the function checkFamilySubfamily returns true if:

1. The new species contains both family and subfamily values
2. These values are not "incertae sedis" or "indet."
3. The values of their parent fields (subclass, order ,suborder) are not "incertae sedis" or "indet."
4. Any existing species has the same subfamily value, but a different family value.

The checkXY functions contain a lot of reused code, and could be simplified as long as they are kept readable.