add ... to classification when using NCBI

related to #890

Author: zachary-foster

R/classification.R

@@ -240,9 +240,9 @@ classification.default <- function(sci_id, db = NULL, callopts = list(),
       stats::setNames(classification(id, return_id = return_id, ...), sci_id)
     },
     ncbi = {
-      id <- process_ids(sci_id, db, get_uid, rows = rows)
+      id <- process_ids(sci_id, db, get_uid, rows = rows, ...)
       stats::setNames(classification(id, callopts = callopts,
-        return_id = return_id), sci_id)
+        return_id = return_id, ...), sci_id)
     },
     eol = {
       id <- process_ids(sci_id, db, get_eolid, rows = rows, ...)

R/get_natservid.R

@@ -80,7 +80,7 @@ get_natservid <- function(sci_com, searchtype = "scientific", ask = TRUE,
   assert(ask, "logical")
   assert(messages, "logical")
   assert_rows(rows)
-  if (!is.null(commnames)) {
+  if (!is.null(query)) {
     lifecycle::deprecate_warn(when = "v0.9.97", what = "get_natservid(query)", with = "get_natservid(sci_com)")
     sci_com <- query
   }

R/get_uid.R

@@ -411,7 +411,7 @@ get_uid_ <- function(sci_com, messages = TRUE, rows = NA, key = NULL,
 
   key <- getkey(key, "ENTREZ_KEY")
   if (!is.null(sciname)) {
-    lifecycle::deprecate_warn(when = "v0.9.97", what = "get_uid_(sciname)", with = "get_uid_(sci_com)")
+  lifecycle::deprecate_warn(when = "v0.9.97", what = "get_uid_(sciname)", with = "get_uid_(sci_com)")
     sci_com <- sciname
   }