Merge pull request #51 from stitam/webhis2

Do not use web histories by default with ncbi_link_uid()

Author: stitam

R/ncbi_link_uid.R

@@ -38,6 +38,9 @@
 #' However, if it is specified, it must be identical to the \code{db} attribute
 #' of the \code{"ncbi_uid"} object. If query is a character vector, the
 #' \code{from} argument is required.
+  #' @note \code{ncbi_link_uid()} can work with or without web histories, but the
+#' behaviour of the function with web histories is unreliable. The option is
+#' there but it is recommended NOT to use web histories with this function.
 #' @examples
 #' \dontrun{
 #' ncbi_link_uid("4253631", "assembly", "biosample")
@@ -49,7 +52,7 @@ ncbi_link_uid <- function(
     from = NULL,
     to,
     batch_size = 100,
-    use_history = TRUE,
+    use_history = FALSE,
     verbose = getOption("verbose")
     ) {
   if ("ncbi_uid" %in% class(query)) {

man/ncbi_link_uid.Rd

@@ -4,7 +4,7 @@ test_that("ncbi_link_uid() converts using input history", {
   # input is ncbi_uid object with history
   assembly_uid <- ncbi_get_uid(examples$assembly, db = "assembly")
   biosample_uid <- ncbi_link_uid(
-    assembly_uid, from = "assembly", to = "biosample"
+    assembly_uid, from = "assembly", to = "biosample", use_history = TRUE
   )
   expect_true(all(c("ncbi_uid", "list") %in% class(biosample_uid)))
   expect_true(all(biosample_uid$uid %in% c("2952905", "1730125")))