@@ -346,16 +346,19 @@ barcodeToUUID <-

 #' @rdname ID-translation

 #'

-#' @param filenames character() A vector of file names usually obtained

+#' @param filenames `character()` A vector of file names usually obtained

 #'     from a `GenomicDataCommons` query

 #'

-#' @param slides logical(1L) Whether the provided file names correspond to

-#'   slides typically with an `.svs` extension. **Note** The barcodes returned

-#'   correspond 1:1 with the `filename` inputs. Always triple check the

-#'   output against the Genomic Data Commons Data Portal by searching the

-#'   file name and comparing associated "Entity ID" with the `submitter_id`

+#' @param slides `logical(1L)` **DEPRECATED**: Whether the provided file names

+#'   correspond to slides typically with an `.svs` extension. **Note** The

+#'   barcodes returned correspond 1:1 with the `filename` inputs. Always triple

+#'   check the output against the Genomic Data Commons Data Portal by searching

+#'   the file name and comparing associated "Entity ID" with the `submitter_id`

 #'   given by the function.

 #'

+#' @details When providing slide file names, the function will only work if

+#'   **all** the provided files are slide files with an `.svs` extension.

+#'

 #' @examples

 #' library(GenomicDataCommons)

 #'

@@ -386,6 +389,19 @@ barcodeToUUID <-

 #'

 #' @export filenameToBarcode

 filenameToBarcode <- function(filenames, slides = FALSE) {

+    endwithsvs <- endsWith(filenames, "svs")

+    if (!all(endwithsvs) && any(endwithsvs))

+        stop("Not all file names have an 'svs' extension.")

+    if (!missing(slides)) {

+        .Deprecated(

+            msg = "The 'slides' argument is deprecated.", package = "TCGAutils"

+        )

+        if (all(endwithsvs) && !slides)

+            warning(

+                "All files have an 'svs' extension. Setting 'slides' to TRUE."

+            )

+        slides <- all(endwithsvs)

+    }

     filesres <- files()

     endpoint <- "cases.samples.portions.analytes.aliquots.submitter_id"

     reselem <- "cases"

@@ -31,14 +31,14 @@ type of \code{id_vector} entered (default \code{"case_id"})}

 \item{barcodes}{character() A vector of TCGA barcodes}

-\item{filenames}{character() A vector of file names usually obtained

+\item{filenames}{\code{character()} A vector of file names usually obtained

 from a \code{GenomicDataCommons} query}

-\item{slides}{logical(1L) Whether the provided file names correspond to

-slides typically with an \code{.svs} extension. \strong{Note} The barcodes returned

-correspond 1:1 with the \code{filename} inputs. Always triple check the

-output against the Genomic Data Commons Data Portal by searching the

-file name and comparing associated "Entity ID" with the \code{submitter_id}

+\item{slides}{\code{logical(1L)} \strong{DEPRECATED}: Whether the provided file names

+correspond to slides typically with an \code{.svs} extension. \strong{Note} The

+barcodes returned correspond 1:1 with the \code{filename} inputs. Always triple

+check the output against the Genomic Data Commons Data Portal by searching

+the file name and comparing associated "Entity ID" with the \code{submitter_id}

 given by the function.}

 \item{id}{character(1) A UUID whose history of versions is sought}

@@ -70,6 +70,9 @@ Based on the file UUID supplied, the appropriate entity_id (TCGA barcode) is

 returned. In previous versions of the package, the 'end_point' parameter

 would require the user to specify what type of barcode needed. This is no

 longer supported as \code{entity_id} returns the appropriate one.

+

+When providing slide file names, the function will only work if

+\strong{all} the provided files are slide files with an \code{.svs} extension.

 }

 \examples{

 ## Translate UUIDs >> TCGA Barcode