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Assemble the whole consolidated core from the ingest shards

Source: R/shards.R
assemble_core.Rd

Convenience wrapper: sample, obs, obs_attribute, sample_measurement (surrogate ids renumbered globally), the supplemental obs_ctd_full, and the taxa references (taxon merged with priority; dataset_taxon /taxon_group deduplicated). Errors if sample_key is not globally unique — the namespacing guarantee the whole model rests on.

Usage

assemble_core(
  con,
  root = ".",
  supplemental = TRUE,
  parquet_dir = cc_stage_path("parquet"),
  exclude = release_excluded_datasets(root)
)

Arguments

con

a DuckDB connection

root

workflows repo root

supplemental

TRUE (default) to include every supplemental full-resolution table the ingests declare, FALSE for none, or an explicit character vector of table names. See supplemental_core_tables().

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; defaults to the ingests declaring calcofi.in_release: false (see release_excluded_datasets()). Resolved once here and threaded to every shard read.

Value

(invisibly) a named list of row counts