Stage the QC reference tables a rule registry expects

The rules join against reference data that is deliberately NOT part of the release: the quality-code vocabulary, the harmonic climatology and station bottom depths mined from the CalCOFI hydrographic Access master, and a seafloor depth per cast derived from bathymetry. This puts all of them on one connection so both the app and the ingest notebook get the same reference inputs.

Usage

qc_stage_reference(
  con,
  dir_workflows,
  gebco_tif = NULL,
  sample_tbl = "sample",
  quiet = FALSE
)

Arguments

con

a DBI connection to stage into

dir_workflows

root of the CalCOFI/workflows checkout

gebco_tif

optional path to a positive-down bathymetry GeoTIFF (the one apps/ctd-viz crops from GEBCO 2025). When supplied — and when terra is installed — sample_seafloor is built by extracting it at each cast position.

sample_tbl

table or view holding sample_key / longitude / latitude

quiet

suppress the per-table progress lines

Value

character vector of the tables actually staged, invisibly

Details

measurement_type comes from the WORKFLOWS REGISTRY, not from a release: the registry is the source of truth and moves ahead of the release (valid_min / valid_max existed there before any release carried them), so sourcing it from a release would silently disable every range rule.

A missing input is left as a MISSING TABLE rather than an empty one. An empty reference table makes its rules return zero rows, which reads as "clean"; a missing table makes them error, which reads as "not checked". The second is the truth.