Cruises that carry samples but no observations — the silent-loss guard

A cruise can leave obs without leaving sample, and nothing about that violates a foreign key: FK validation runs child -> parent, so every surviving obs row still has a parent, and a parent with no children breaks no constraint. Release v2026.08.08 shipped in exactly that state — 10 calcofi_ctd-cast cruises kept all 1,186 of their casts and lost all 874,000 of their observations, because a Google Drive placeholder read as zero rows and the direction letter the thinning step needs came from the filename of a conflict copy. No check anywhere looked at the parent side.

Usage

check_cruise_coverage(
  con,
  obs_tbl = "obs",
  max_orphan_cruises = 0L,
  halt = TRUE,
  verbose = TRUE
)

Arguments

con

a DBI connection holding sample and obs

obs_tbl

name of the observation table (default "obs")

max_orphan_cruises

integer allowance, or a named integer vector keyed by dataset_key for a per-dataset ratchet. Use 0 where the correct answer is known to be zero (an ingest asserting its own output); use the current counts as a ratchet at release time so a new orphan fails while a documented backlog does not. May only ever be lowered.

halt

logical; stop() when the allowance is exceeded (default TRUE)

verbose

logical; message the summary

Value

a data.frame, one row per dataset_key, with cruises, cruises_no_obs, orphan_samples and emits_obs (invisibly when verbose = FALSE)

Details

The grain is the cruise, deliberately, and it is not the sample. A CTD sample row is one physical cast per direction while obs keeps a single direction, so about half of calcofi_ctd-cast's cast rows legitimately carry no observations and a per-sample assertion would be wrong on arrival. A whole cruise with none is never legitimate.

A dataset that emits no observations at all is exempt rather than failing 587 times: sio_pic-zooplankton is a net-tow registry whose biovolumes are still pending from the provider, so contributing sample alone is its designed state. The rule is therefore relative — if a dataset contributes observations, every one of its cruises must — which needs no allowlist to say so.