feat(taxonomy): Host organism categories endpoint

[maverbiest]

As a follow-up to host validation, we would like to add functionality to loculus to assign host organisms to configurable categories.

These categories could then be used for filtering sequences in the front-end; e.g., it would be nice for arboviruses if people are able to select "Mosquito" from a drop-down menu to get all sequences that were obtained from any mosquito species.

Implementation & configuration

This PR adds a /taxa/{tax_id}/host-categories endpoint to the taxonomy-service. This endpoint returns a list of host category lables that apply to the provided tax_id.

The labels are configured like this (obviously not labels we'd use):

organism_categories:
  7157: "BZZZZZ" # Culicidae
  131567: "I'm a cellular organism!" # Cellular organisms
  2759: "I'm a Eukaryote!" # Eukaryota

The keys in organism_categories are NCBI taxon IDs, the values are host category lables. When provided with a tax_id, the endpoint will return all labels associated with taxa inorganism_categories that are an ancestor of tax_id.

For this to be useable in loculus/pathoplexus, we'd need to add functionality to assign host categories to each sequence during preprocessing (would be a separate PR).

Usage

When using the example configuration shown above, the following results are returned (taxonomy-service running locally in a docker container):

Aedes aegypti (7159) and Culex pipiens (7157) are mosquitos:

➜  taxonomy_service git:(host-organism-categories) curl localhost:5000/taxa/7159/host-categories
["BZZZZZ","I'm a Eukaryote!","I'm a cellular organism!"]%                                                                                                                                                                                                                                                                                                                                                                                    

➜  taxonomy_service git:(host-organism-categories) curl localhost:5000/taxa/7175/host-categories
["BZZZZZ","I'm a Eukaryote!","I'm a cellular organism!"]%

Humans (9606) are not mosquitos:

➜  taxonomy_service git:(host-organism-categories) ✗ curl localhost:5000/taxa/9606/host-categories
["I'm a Eukaryote!","I'm a cellular organism!"]%

Yersinia pestis (632) is not a eukaryote:

➜  taxonomy_service git:(host-organism-categories) ✗ curl localhost:5000/taxa/632/host-categories
["I'm a cellular organism!"]%

The root is nothing:

➜  taxonomy_service git:(host-organism-categories) ✗ curl localhost:5000/taxa/1/host-categories
[]%

Alternatives

An alternative way to get this functionality may be to use custom taxonomic lineage files and filter via SILO/LAPIS. This is something I'm scoping out currently.

PR Checklist

• All necessary documentation has been adapted.
• The implemented feature is covered by appropriate, automated tests.
• Any manual testing that has been done is documented (i.e. what exactly was tested?)

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