fix #115 - taxa_search only ncbi for now, stop() on db=traitbank for now

use messages param instead of verbose passed to get_uid internally within ncbi_searcher

R/ncbi_searcher.R

@@ -74,7 +74,7 @@ ncbi_searcher <- function(taxa = NULL, id = NULL, seqrange="1:3000",
 
   # Convert 'taxa' to 'id' if 'taxa' is supplied ---------------------------------------------------
   if (is.null(id)) {
-    id <- get_uid(taxa, verbose = verbose)
+    id <- get_uid(taxa, messages = verbose)
     names(id) <- taxa
   } else {
     id <- as.character(id)
@@ -185,12 +185,12 @@ get_parent <- function(id, verbose) {
     ancestry <- classification(id = id, db = "ncbi")[[1]]
     if (nrow(ancestry) > 1) {
       parent_name <- ancestry$name[nrow(ancestry) - 1]
-      return(get_uid(parent_name, verbose = verbose))
+      return(get_uid(parent_name, messages = verbose))
     }
   }
   if (!is.null(names(id)) && grepl(" ", names(id))) { #if a name is given and looks like a species
     parent_name <- strsplit(names(id), " ")[[1]][[1]]
-    return(get_uid(parent_name, verbose = verbose))
+    return(get_uid(parent_name, messages = verbose))
   }
   return(NA)
 }

R/taxa_search.R

@@ -2,12 +2,12 @@
 #'
 #' @export
 #' @param x (character) Taxonomic name(s) to search for
-#' @param db (character) One of betydb, traitbank, ncbi, coral.
+#' @param db (character) only 'ncbi' for now - other options
+#' maybe in the future
 #' @param ... Curl options passed on to \code{\link[httr]{GET}}
 #' @return A \code{data.frame}
 #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com}
 #' @examples \dontrun{
-#' taxa_search("Poa annua", db = "traitbank")
 #' taxa_search("Poa annua", db = "ncbi")
 #' }
 taxa_search <- function(x, db, ...) {
@@ -26,8 +26,9 @@ taxa_search.character <- function(x, db, ...) {
   }
   switch(db,
     traitbank = {
-      id <- get_tb(x)
-      traitbank(pageid = id, ...)
+      stop("traitbank not working for now; see ?traits::traitbank")
+      # id <- get_tb(x)
+      # traitbank(pageid = id, ...)
     },
     ncbi = {
       ncbi_searcher(taxa = x, ...)