Every dataset a taxon registry names must be one some dataset supplies
Source:R/check.R
check_taxon_registries.Rdmetadata/taxon_override.csv and metadata/taxon_group.csv are read whole
by every ingest while each loads only its own vocabulary, so a row for
another dataset is normal there and cannot be validated. This is the check
for the place where every dataset IS present — the release, after
assemble_core() — replacing the hard-coded list of dataset names the
package used to validate against (taxon plan D5). The allowed set is the
dataset_keys present in dataset_taxon ∪ measurement_taxon; a row naming
anything else (a typo, a retired dataset) errors, because a registry row that
matches nothing is how a missing id hides.
Usage
check_taxon_registries(
con,
overrides = NULL,
group_rules = NULL,
measurement_taxon = NULL,
halt = TRUE
)Arguments
- con
a DBI connection holding the assembled
dataset_taxon- overrides
the override registry (
metadata/taxon_override.csv), or NULL- group_rules
the group registry (
read_taxon_group_rules()), or NULL- measurement_taxon
the composite crosswalk (
metadata/measurement_taxon.csv), whosedataset_keys count as supplied, or NULL- halt
logical;
stop()on an orphan (defaultTRUE)