Rename ncbi_supported_dbs() to ncbi_dbs()

R/link_uid.R

@@ -6,12 +6,12 @@
 #' This function links uids from one database with uids from another.
 #' @param query character; a vector of uids.
 #' @param from character; the database the queried uids come from.
-#' \code{ncbi_supported_dbs()} lists all available options.
+#' \code{ncbi_dbs()} lists all available options.
 #' @param to character; the database in which the function should look for links.
 #' @param cache_file character; the name of the cache file without the file
 #' extension. If \code{NULL}, results are not cached.
 #' @param verbose logical; should verbos messages be printed to the console?
-#' \code{ncbi_supported_dbs()} lists all available options.
+#' \code{ncbi_dbs()} lists all available options.
 #' @return A tibble
 #' @examples
 #' \dontrun{
@@ -27,8 +27,8 @@ link_uid <- function(query,
   if (any(is.na(as.numeric(query)))) {
     stop("Query must be a valid UID. Valid UIDs can be converted to 'numeric'.")
   }
-  from <- match.arg(from, ncbi_supported_dbs())
-  to <- match.arg(to, ncbi_supported_dbs())
+  from <- match.arg(from, ncbi_dbs())
+  to <- match.arg(to, ncbi_dbs())
   foo <- function(x) {
     if (verbose) webseq_message("query", x, appendLF = FALSE)
     res <- NULL

R/ncbi_supported_dbs.R → R/ncbi_dbs.R

@@ -1,4 +1,4 @@
-ncbi_supported_dbs <- function() {
+ncbi_dbs <- function() {
   if (!dir.exists(tempdir())) dir.create(tempdir())
   if (!file.exists(paste0(tempdir(), "/webseq.rds"))) {
     dbs <- rentrez::entrez_dbs()

R/ncbi_get_meta.R

@@ -3,7 +3,7 @@
 #' This function retrieves metadata from a given NCBI sequence database.
 #' @param term character; one or more search terms.
 #' @param db character; the database to search in. For options see
-#' \code{ncbi_supported_dbs()}. Not all databases are supported.
+#' \code{ncbi_dbs()}. Not all databases are supported.
 #' @param batch_size integer; the number of search terms to query at once. If
 #' the number of search terms is larger than \code{batch_size}, the search terms
 #' are split into batches and queried separately.
@@ -34,7 +34,7 @@ ncbi_get_meta <- function(
     parse = TRUE,
     verbose = getOption("verbose")
   ) {
-  db <- match.arg(db, choices = ncbi_supported_dbs())
+  db <- match.arg(db, choices = ncbi_dbs())
   uids <- ncbi_get_uid(
     term = term,
     db = db,

R/ncbi_get_uid.R

@@ -6,7 +6,7 @@
 #' in other NCBI databases or to retrieve the data itself.
 #' @param term character; one or more search terms.
 #' @param db character; the database to search in. For options see
-#' \code{ncbi_supported_dbs()}
+#' \code{ncbi_dbs()}
 #' @param batch_size integer; the number of search terms to query at once. If
 #' the number of search terms is larger than \code{batch_size}, the search terms
 #' are split into batches and queried separately.
@@ -36,7 +36,7 @@ ncbi_get_uid <- function(
     use_history = TRUE,
     verbose = getOption("verbose")
     ) {
-  db <- match.arg(db, choices = ncbi_supported_dbs())
+  db <- match.arg(db, choices = ncbi_dbs())
   if (all(is.na(term))) {
     stop("No valid search terms.")
   } else if (any(is.na(term))){

tests/testthat/test-ncbi_get_meta.R

@@ -8,7 +8,7 @@ test_that("ncbi_get_meta() works with Microthrix parvicella", {
 test_that("ncbi_get_meta() works with all supported dbs", {
   data(examples)
 
-  expect_true(all(names(examples) %in% ncbi_supported_dbs()))
+  expect_true(all(names(examples) %in% ncbi_dbs()))
 
   for (i in names(examples)) {
     res <- suppressWarnings(ncbi_get_meta(examples[[i]], db = i, parse = FALSE))