update gna_parse to new api

NAMESPACE

@@ -243,10 +243,11 @@ export(get_wormsid)
 export(get_wormsid_)
 export(getkey)
 export(gisd_isinvasive)
-export(gn_parse)
+export(gna_parse)
+export(gna_search)
 export(gni_details)
 export(gni_parse)
-export(gni_search)
+export(gni_seach)
 export(gnr_datasources)
 export(gnr_resolve)
 export(id2name)

R/gbif_parse.R

@@ -8,7 +8,7 @@
 #' all species names in `scientificname`.
 #' @author John Baumgartner \email{johnbb@@student.unimelb.edu.au}
 #' @references https://www.gbif.org/tools/name-parser/about
-#' @seealso [gni_parse()], [gn_parse()]
+#' @seealso [gni_parse()], [gna_parse()]
 #' @examples \dontrun{
 #' gbif_parse(scientificname='x Agropogon littoralis')
 #' gbif_parse(c('Arrhenatherum elatius var. elatius',

R/gn_parse.R → R/gna_parse.R

@@ -8,43 +8,53 @@
 #' @seealso [gbif_parse()], [gni_parse()]
 #' @references http://gni.globalnames.org/
 #' @examples \dontrun{
-#' gn_parse("Cyanistes caeruleus")
-#' gn_parse("Plantago minor")
-#' gn_parse("Plantago minor minor")
-#' gn_parse(c("Plantago minor minor","Helianthus annuus texanus"))
+#' gna_parse("Cyanistes caeruleus")
+#' gna_parse("Plantago minor")
+#' gna_parse("Plantago minor minor")
+#' gna_parse(c("Plantago minor minor","Helianthus annuus texanus"))
 #' 
 #' # if > 20 names, uses an HTTP POST request
 #' x <- names_list("species", size = 30)
-#' gn_parse(x)
+#' gna_parse(x)
 #'
 #' # pass on curl options
-#' gn_parse("Cyanistes caeruleus", verbose = TRUE)
+#' gna_parse("Cyanistes caeruleus", verbose = TRUE)
 #' }
-gn_parse <- function(names, ...) {
+gna_parse <- function(names, ...) {
   assert(names, "character")
   method <- ifelse(length(names) <= 20, "get", "post")
-  tmp <- gn_http(method, names, ...)
+  tmp <- gna_http(method, names, ...)
   out <- jsonlite::fromJSON(tmp)
   out[paste0('canonical_', colnames(out$canonical))] <- out$canonical
   out$canonical <- NULL
   tibble::as_tibble(out)
 }
 
-gn_http <- function(method, names, ...) {
-  cli <- crul::HttpClient$new("https://parser.globalnames.org",
+gna_http <- function(method, names, ...) {
+  cli <- crul::HttpClient$new("https://parser.globalnames.org/api/v1/",
     headers = tx_ual, opts = list(...))
   res <- switch(method,
     get = {
-      names <- paste0(names, collapse = "|")
-      # args <- list(q = names)
-      cli$get(paste0("api/v1/", names))
+      cli$get(paste0('api/v1/', paste0(names, collapse = "|")))
     },
     post = {
       cli$headers <- c(cli$headers, list(`Content-Type` = "application/json",
-        Accept = "application/json"))
-      cli$post("api", body = jsonlite::toJSON(names))
+        accept = "application/json"))
+      cli$post(body = jsonlite::toJSON(list(names = names)))
     }
   )
   res$raise_for_status()
   res$parse("UTF-8")
 }
+
+
+#' Parse scientific names using EOL's name parser.
+#'
+#' THIS FUNCTION IS DEFUNCT.
+#' 
+#' @export
+#' @keywords internal
+gni_parse <- function(names, ...) {
+  .Defunct("ncbi_searcher", "traits",
+           msg = "This function is defunct. See gna_parse()")
+}

R/gna_search.R

@@ -0,0 +1,80 @@
+#' @title Search for taxonomic names using the Global Names Architecture
+#'
+#' @description Uses the Global Names Index, see http://gni.globalnames.org
+#'
+#' @export
+#' @param sci (character) required. Name pattern you want to search
+#' for. WARNING: Does not work for common names. Search term may include
+#' following options:
+#'
+#' * `n`: A shortcut that allows to put together several elements (e.g., `n:B. bubo Linn. 1750-1800`)
+#' * `g`: a genus name. (e.g. `g:B.`, `g:Bub.`, `g:Bubo`)
+#' * `isp`: an infraspecies name (e.g. `sp:bubo`, `sp:gallop.`)
+#' * `asp`: either species or infraspecies (all sp) (e.g. `asp:bubo`)
+#' * `ds`: data-sources IDs (e.g., `ds:1,2,3`)
+#' * `tx`: parent taxon . Uses classification of the first data-source from `ds`. If data-sources are not set, uses Catalogue of Life. (e.g. `tx:Aves`)
+#' * `au`: author - Search by author word	(e.g. `au:Linnaeus`, `au:Linn.`)
+#' * `y`: year - Search by year (e.g. `y:2005`)
+#'
+#' @param justtotal Return only the total results found.
+#' @param ... Curl options passed on to [crul::verb-GET]
+#' @author Scott Chamberlain, Zachary Foster
+#' @return data.frame of results.
+#' @seealso [gnr_datasources()], [gna_search()]
+#' @keywords globalnamesindex names taxonomy
+#' @references http://gni.globalnames.org/
+#' https://apidoc.globalnames.org/gnames
+#' 
+#' @examples \dontrun{
+#' gna_search('n:B. bubo ds:1,2 au:Linn. y:1700-')
+#' }
+gna_search <- function(sci, justtotal = FALSE, parse_names = FALSE, 
+                       per_page = NULL, page = NULL, search_term = NULL, ...) {
+
+  query <- tc(list(search_term = sci))
+  cli <- crul::HttpClient$new('https://verifier.globalnames.org',
+                              headers = tx_ual, opts = list(...))
+  tt <- cli$get(path = paste0('/api/v1/search/', curl::curl_escape(sci)))
+  tt$raise_for_status()
+  out <- jsonlite::fromJSON(tt$parse("UTF-8"), FALSE)
+  if (justtotal) {
+    return(out$metadata$namesNumber)
+  } else {
+    df <- do.call(rbind, lapply(out$names, function(x) {
+      all_feilds <- unlist(x)
+      names(all_feilds) <- vapply(strsplit(names(all_feilds), split = '.', fixed = TRUE), function(x) x[length(x)], FUN.VALUE = character(1))
+      all_feilds <- all_feilds[! duplicated(names(all_feilds))]
+      return(as.data.frame(as.list(all_feilds)))
+    }))
+    df <- colClasses(df, "character")
+    df <- tibble::as_tibble(df)
+    if (NROW(df) != 0) {
+      names(df) <- c("id", "name", "cardinality", "matchType", "dataSourceId", "dataSourceTitleShort", 
+                     "curation", "recordId", "outlink", "entryDate", "sortScore", 
+                     "matchedNameID", "matchedName", "matchedCardinality", "currentRecordId", 
+                     "currentNameId", "currentName", "currentCardinality", "currentCanonicalSimple", 
+                     "currentCanonicalFull", "taxonomicStatus", "isSynonym", "classificationPath", 
+                     "classificationRanks", "classificationIds", "editDistance", "stemEditDistance", 
+                     "cardinalityScore", "infraSpecificRankScore", "fuzzyLessScore", 
+                     "curatedDataScore", "authorMatchScore", "acceptedNameScore", 
+                     "parsingQualityScore", "dataSourcesNum", "dataSourcesIds")
+    }
+
+    if (parse_names) {
+      data.frame(df, gni_parse(as.character(df$name)), stringsAsFactors = FALSE)
+    } else {
+      df
+    }
+  }
+}
+
+#' Search for taxonomic names using the Global Names Index
+#'
+#' THIS FUNCTION IS DEFUNCT.
+#' 
+#' @export
+#' @keywords internal
+gni_seach <- function(names, ...) {
+  .Defunct("ncbi_searcher", "traits",
+           msg = "This function is defunct. See gna_search()")
+}

R/gni_details.R

@@ -9,7 +9,7 @@
 #' @param ... Curl options passed on to [crul::verb-GET]
 #' @author Scott Chamberlain
 #' @return Data.frame of results.
-#' @seealso [gnr_datasources()], [gni_search()].
+#' @seealso [gnr_datasources()], [gna_search()].
 #' @keywords globalnamesindex names taxonomy
 #' @examples \dontrun{
 #' gni_details(id = 17802847)

R/gni_verifier.R

@@ -24,90 +24,3 @@
 
 
 
-#' @title Search for taxonomic names using the Global Names Index
-#'
-#' @description Uses the Global Names Index, see http://gni.globalnames.org
-#'
-#' @export
-#' @param sci (character) required. Name pattern you want to search
-#' for. WARNING: Does not work for common names. Search term may include
-#' following options:
-#'
-#' * `n`: A shortcut that allows to put together several elements (e.g., `n:B. bubo Linn. 1750-1800`)
-#' * `g`: a genus name. (e.g. `g:B.`, `g:Bub.`, `g:Bubo`)
-#' * `isp`: an infraspecies name (e.g. `sp:bubo`, `sp:gallop.`)
-#' * `asp`: either species or infraspecies (all sp) (e.g. `asp:bubo`)
-#' * `ds`: data-sources IDs (e.g., `ds:1,2,3`)
-#' * `tx`: parent taxon . Uses classification of the first data-source from `ds`. If data-sources are not set, uses Catalogue of Life. (e.g. `tx:Aves`)
-#' * `au`: author - Search by author word	(g.g. `au:Linnaeus`, `au:Linn.`)
-#' * `y`: year - Search by year (e.g. `y:2005`)
-#'
-#' @param justtotal Return only the total results found.
-#' @param parse_names If `TRUE`, use [gni_parse()] to parse
-#' @param per_page Number of items per one page (numbers larger
-#' than 1000 will be decreased to 1000) (default is 30).
-#' @param page Page number you want to see (default is 1).
-#' names. Default: `FALSE`
-#' @param search_term Deprecated, see `sci`
-#' @param ... Curl options passed on to [crul::verb-GET]
-#' @author Scott Chamberlain, Zachary Foster
-#' @return data.frame of results.
-#' @seealso [gnr_datasources()], [gni_search()]
-#' @keywords globalnamesindex names taxonomy
-#' @references http://gni.globalnames.org/
-#' https://apidoc.globalnames.org/gnames
-#' 
-#' @examples \dontrun{
-#' gni_search('n:B. bubo ds:1,2 au:Linn. y:1700-')
-#' }
-gni_search <- function(sci, justtotal = FALSE, parse_names = FALSE, 
-                       per_page = NULL, page = NULL, search_term = NULL, ...) {
-
-  if (!is.null(search_term)) {
-    lifecycle::deprecate_warn(when = "v0.9.97", what = "gni_search(search_term)", with = "gni_search(sci)")
-    sci <- search_term
-  }
-  if (!is.null(per_page)) {
-    lifecycle::deprecate_warn(when = "v0.9.97", what = "gni_search(per_page)")
-  }
-  if (!is.null(page)) {
-    lifecycle::deprecate_warn(when = "v0.9.97", what = "gni_search(page)")
-  }
-
-  query <- tc(list(search_term = sci))
-  cli <- crul::HttpClient$new('https://verifier.globalnames.org',
-                               headers = tx_ual, opts = list(...))
-  tt <- cli$get(path = paste0('/api/v1/search/', curl::curl_escape(sci)))
-  tt$raise_for_status()
-  out <- jsonlite::fromJSON(tt$parse("UTF-8"), FALSE)
-
-  if (justtotal) {
-    return(out$metadata$namesNumber)
-  } else {
-    df <- do.call(rbind, lapply(out$names, function(x) {
-      all_feilds <- unlist(x)
-      names(all_feilds) <- vapply(strsplit(names(all_feilds), split = '.', fixed = TRUE), function(x) x[length(x)], FUN.VALUE = character(1))
-      all_feilds <- all_feilds[! duplicated(names(all_feilds))]
-      return(as.data.frame(as.list(all_feilds)))
-    }))
-    df <- colClasses(df, "character")
-    df <- tibble::as_tibble(df)
-    if (NROW(df) != 0) {
-      names(df) <- c("id", "name", "cardinality", "matchType", "dataSourceId", "dataSourceTitleShort", 
-                     "curation", "recordId", "outlink", "entryDate", "sortScore", 
-                     "matchedNameID", "matchedName", "matchedCardinality", "currentRecordId", 
-                     "currentNameId", "currentName", "currentCardinality", "currentCanonicalSimple", 
-                     "currentCanonicalFull", "taxonomicStatus", "isSynonym", "classificationPath", 
-                     "classificationRanks", "classificationIds", "editDistance", "stemEditDistance", 
-                     "cardinalityScore", "infraSpecificRankScore", "fuzzyLessScore", 
-                     "curatedDataScore", "authorMatchScore", "acceptedNameScore", 
-                     "parsingQualityScore", "dataSourcesNum", "dataSourcesIds")
-    }
-
-    if (parse_names) {
-      data.frame(df, gni_parse(as.character(df$name)), stringsAsFactors = FALSE)
-    } else {
-      df
-    }
-  }
-}

R/gnr_datasources.R

@@ -6,7 +6,7 @@
 #' @param ... Curl options passed on to [crul::HttpClient]
 #' @param todf defunct, always get a data.frame back now
 #' @return data.frame/tibble
-#' @seealso [gnr_resolve()], [gni_search()]
+#' @seealso [gnr_resolve()], [gna_search()]
 #' @keywords resolve names taxonomy
 #' @references https://resolver.globalnames.org/data_sources
 #' @examples \dontrun{

R/iucn_getname.R

@@ -24,7 +24,7 @@
 #' }
 iucn_getname <- function(name, verbose = TRUE, ...) {
   mssg(verbose, "searching Global Names ...")
-  all_names <- gni_search(sci = name, parse_names = TRUE)
+  all_names <- gna_search(sci = name, parse_names = TRUE)
   if (NROW(all_names) == 0) {
     stop("No names found matching ", name, call. = FALSE)
   }

R/taxize-package.R

@@ -74,7 +74,6 @@
 #' @importFrom cli symbol cat_line rule
 #' @name taxize-package
 #' @aliases taxize
-#' @docType package
 #' @author Scott Chamberlain 
 #' @author Eduard Szoecs \email{eduardszoecs@@gmail.com}
 #' @author Zachary Foster \email{zacharyfoster1989@@gmail.com}

R/taxize_cite.R

@@ -132,7 +132,7 @@ data_citations <- function(x){
     gisd_isinvasive = list(gisd = c_gisd),
     gni_details = list(gni = c_gni),
     gni_parse = list(gni = c_gni),
-    gni_search = list(gni = c_gni),
+    gna_search = list(gni = c_gni),
     gnr_datasources = list(global_names = c_gnames),
     gnr_resolve = list(global_names = c_gnames),
     iplant_resolve = list(iplant = c_iplant),