Prune the taxa references to one dataset's shard

build_taxon_reference() / build_dataset_taxon() / build_taxon_group() read whichever taxon sources are present in con, which inside an ingest is normally just that dataset's vocabulary — but not always. An ingest may have loaded another dataset's tables as references, and swfsc_ichthyo holds a WoRMS lineage hierarchy (build_taxon_hierarchy()) that is broader than the taxa its own observations reach. This trims all three to this dataset's shard so the release union stays small and the shards stay disjoint-ish.

Usage

prune_taxon_shard(con, dataset_key)

Arguments

con

a DuckDB connection holding taxon / dataset_taxon (and optionally taxon_group) as built by the three builders

dataset_key

provider_dataset to keep

Value

(invisibly) a named list of the surviving row counts

Details

Lineage ancestors are kept: descendant expansion walks parent_taxon_key, so dropping an ancestor would break the chain. The kept set is therefore the transitive parent closure of dataset_taxon.taxon_key, not just the directly-referenced taxa.

Generic — there is nothing dataset-specific here beyond the dataset_key argument. Call it after the three builders in an ingest that either holds a hierarchy table or has other datasets' vocabulary tables in scope.