Merge the per-dataset taxon shards into one authoritative reference

Each ingest emits the taxon rows its own vocabulary reaches. The same taxon can appear in several shards (Appendicularia is in both zoodb and zooscan), so rows are collapsed on taxon_key and each field takes the first non-NULL value by source priority — the WoRMS-lineage-bearing shard (swfsc_ichthyo, which carries the hierarchy) first, then the curated seabird/mammal and plankton vocabularies, then everything else. This reproduces the coalescing build_taxon_reference() did when it saw every source at once.

Usage

merge_taxon_shards(
  con,
  root = ".",
  priority = c("swfsc_ichthyo", "farallon_bird-mammal", "cce-lter_zoodb",
    "cce-lter_zooscan", "calcofi_phytoplankton"),
  parquet_dir = cc_stage_path("parquet"),
  exclude = release_excluded_datasets(root)
)

Arguments

con

a DuckDB connection

root

workflows repo root

priority

dataset dirs in descending priority

parquet_dir

directory holding the per-dataset output dirs. Defaults to the local staging root (see cc_stage_dir()), where the bulk parquet lives; an absolute path is used as-is, a relative one is resolved against root. The JSON sidecars stay in the repo and are found separately.

exclude

dataset dir names to skip (see core_shard_paths())

Value

(invisibly) the row count of the merged taxon