taxize::gnr* issues

[cmbappleby]

I'm trying to use EMLassemblyline::template_taxonomic_coverage(), and I get "Error: Service Unavailable (HTTP 503)". After some digging, it seems that resolver.globalnames.org is no longer working and has been replaced with verifier.globalnames.org. The taxize package has a function, gna_verifier() to replace gnr_resolve(); however, there does not appear to be a function that replaces gnr_datasources(). Not sure if this is a taxomonyCleanr issue or a taxize issue.

[clnsmth]

Thanks for reaching out @cmbappleby.

Which version of EMLassemblyline are you running?

[cmbappleby]

@clnsmth 3.3.5

[cmbappleby]

@clnsmth I cloned taxonomyCleanr and tweaked the code, and I got EMLassemblyline::template_taxonomic_coverage() to work. Not sure if it's exactly how it's supposed to work, but it works.

In get_authority() I replaced gnr_resolve() with:

# Use Global Names Verifier to see if the taxon can be found in data.source
  resp <- suppressWarnings(
    taxize::gna_verifier(
      names = taxon,
      data_sources = as.character(data.source)
    )
  )

And I changed the code in this function:

load_gnr_datasources <- function() {
  # Define the API URL for taxa authorities
  url <- "https://verifier.globalnames.org/api/v1/data_sources"

  # Make the GET request to the API
  response <- httr::GET(url)

  # Parse the response JSON to a list
  taxa_authorities <- jsonlite::fromJSON(httr::content(response, "text"))

  gnr_list <- as.data.frame(taxa_authorities)

  return(gnr_list)
}

I do get a warning No encoding supplied: defaulting to UTF-8 and haven't done any troubleshooting to see what's causing it.

[clnsmth]

Thanks @cmbappleby, I'll take a closer look at this code.

Would you mind checking if this issue persists after installing the latest versions of taxonomyCleanr (v.1.6.6) and EMLassemblyline (v3.5.6).

[cmbappleby]

@clnsmth I'm using the latest version of EMLassemblyline. The code I changed was from v.1.6.6 of taxonomyCleanr, which calls taxize functions that utilize Global Names Resolver, which is no longer working.

From v.1.6.6 of taxonomyCleanr

load_gnr_datasources <- function() {
  gnr_list <- as.data.frame(taxize::gnr_datasources())
  gnr_list$title[gnr_list$id == "3"] <- "ITIS"
  return(gnr_list)
}

get_authority <- function(taxon, data.source){

  # Tell user what authority is being queried
  gnr_list <- load_gnr_datasources()
  use_i <- gnr_list[ , 'id'] == data.source
  message('Searching ', gnr_list[use_i, 'title'],' for "',taxon,'"')

  # User Global Names Resolver to see if the taxon can be found in data.source
  resp <- suppressWarnings(
    taxize::gnr_resolve(sci = taxon,
                        data_source_ids = as.character(data.source),
                        resolve_once = TRUE,
                        canonical = TRUE,
                        best_match_only = TRUE))
  # Parse response and return and first item found
  if (nrow(resp) != 0) {
    res <- list(resolved_name = resp$matched_name2[1],
                authority = gnr_list$title[use_i],
                score = resp$score[1])
    return(res)
  } else {
    res <- list(resolved_name =  NA_character_,
                authority = NA_character_,
                score = NA_character_)
    return(res)
  }
}

[cmbappleby]

@clnsmth gnr_resolve() will be removed with the next update to taxize. They have also created a gna_data_sources() function to replace to gnr_datasources().

[wright13]

@clnsmth gnr_resolve() will be removed with the next update to taxize. They have also created a gna_data_sources() function to replace to gnr_datasources().

Looks like taxize 0.10.0 is out now! https://github.com/ropensci/taxize/releases/tag/v0.10.0