taxa db versioning issues within bdc_query_names_taxadb

[mfidino]

The ``bdc_query_names_taxadb()` function hardcodes database versions here:

bdc/R/bdc_query_names_taxadb.R

Lines 210 to 237 in 3121582

	# Currently available databases and versions
	switch(
	EXPR = db,
	itis = {
	db_version <- 2022
	},
	ncbi = {
	db_version <- 2022
	},
	col = {
	db_version <- 2022
	},
	gbif = {
	db_version <- 2022
	},
	iucn = {
	db_version <- 2019 ### TODO: Change to 2022
	},
	ott = {
	db_version <- 2021
	},
	fb = {
	db_version <- 2019
	},
	tpl = {
	db_version <- 2019
	}
	)

However, downstream in this function there are calls to the function taxadb::taxa_tbl() which has the default argument ofs:

taxa_tbl(
  provider = getOption("taxadb_default_provider", "itis"),
  schema = c("dwc", "common"),
  version = latest_version(),
  db = td_connect()
)

When latest_version() != db_version, bdc_query_names_taxadb() says that all species names were not found in the DB. This can be illustrated with the iucn database (hardcoded to 2019, but the 2022 version is available).

test <- bdc::bdc_query_names_taxadb(
 sci_name = "Sus scrofa", 
  db = "iucn"
)

test

 data.frame(test)
  original_search suggested_name distance    notes taxonID
1      Sus scrofa             NA       NA notFound    <NA>
  scientificName taxonRank acceptedNameUsageID taxonomicStatus
1           <NA>      <NA>                <NA>            <NA>
  kingdom phylum class order family genus specificEpithet
1    <NA>   <NA>  <NA>  <NA>   <NA>  <NA>            <NA>
  vernacularName infraspecificEpithet
1           <NA>                 <NA>

I'm working off the GitHub installation of bdc

[kguidonimartins]

Thanks for reporting @mfidino, and sorry for the late response. GitHub didn't notify me about this issue :/

However, downstream in this function there are calls to the function taxadb::taxa_tbl() which has the default argument ofs:

Nice catch! I included the argument now. Can you test the latest version of {bdc}?

remotes::install_github("brunobrr/bdc", force = TRUE)

We're aware of the latest version of the IUCN database. However, {taxadb} cannot return the latest version in a fit-for-use way yet (see here). That's the only reason to keep the hard-coded database versions.

[kguidonimartins]

Databases are hardcoded for a while in the new bdc release, and the following databases are not available: "tpl", "fb", "slb", "wd", and "iucn". I'm closing this issue due to inactivity. Please feel free to reopen it whenever you need to.