From cc95974ce33003e10b34c5af5f149c8e42c94d3a Mon Sep 17 00:00:00 2001
From: Scott Chamberlain <myrmecocystus@gmail.com>
Date: Fri, 28 Jun 2019 16:38:43 -0700
Subject: [PATCH] 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  | 6 +++---
 R/taxa_search.R    | 9 +++++----
 man/taxa_search.Rd | 4 ++--
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/R/ncbi_searcher.R b/R/ncbi_searcher.R
index e40dc85..40830aa 100644
--- a/R/ncbi_searcher.R
+++ b/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)
 }
diff --git a/R/taxa_search.R b/R/taxa_search.R
index 825f0cf..7101b6a 100644
--- a/R/taxa_search.R
+++ b/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, ...)
diff --git a/man/taxa_search.Rd b/man/taxa_search.Rd
index a04931b..0fedc2c 100644
--- a/man/taxa_search.Rd
+++ b/man/taxa_search.Rd
@@ -9,7 +9,8 @@ taxa_search(x, db, ...)
 \arguments{
 \item{x}{(character) Taxonomic name(s) to search for}
 
-\item{db}{(character) One of betydb, traitbank, ncbi, coral.}
+\item{db}{(character) only 'ncbi' for now - other options
+maybe in the future}
 
 \item{...}{Curl options passed on to \code{\link[httr]{GET}}}
 }
@@ -21,7 +22,6 @@ Search for traits by taxa names
 }
 \examples{
 \dontrun{
-taxa_search("Poa annua", db = "traitbank")
 taxa_search("Poa annua", db = "ncbi")
 }
 }