export and document getCatalog function

Author: LiNk-NY

NAMESPACE

@@ -4,6 +4,7 @@ export(HoverNet)
 export(ProvGiga)
 export(ProvGigaList)
 export(embedding)
+export(getCatalog)
 export(getEmbeddings)
 export(listHoverNet)
 export(listProvGiga)
@@ -47,8 +48,10 @@ importFrom(ggplot2,guides)
 importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_void)
+importFrom(httr2,req_headers)
 importFrom(httr2,req_perform)
 importFrom(httr2,request)
+importFrom(httr2,resp_body_json)
 importFrom(httr2,resp_body_string)
 importFrom(methods,callNextMethod)
 importFrom(methods,is)

R/listFiles.R

@@ -17,6 +17,9 @@
 #' @param level `character(1L)` One of "slide_level" or "tile_level" specifying
 #'   the desired ProvGiga data level. Default is "slide_level".
 #'
+#' @returns `listHoverNet`,`listProvGiga`: A `tibble` listing available HoverNet
+#'   or ProvGigaPath files with `Filename`, `Modified`, and `Size` columns.
+#'
 #' @examplesIf interactive()
 #' ## List available HoverNet data for TCGA-OV
 #' listHoverNet(format = "h5ad")
@@ -52,11 +55,47 @@ listProvGiga <- function(
     table[!grepl("^\\.\\.", table[["Filename"]]), ]
 }
 
-getCatalog <- function(pipeline = c("hovernet", "provgigapath")) {
-    pipeline <- match.arg(pipeline)
-    catalog_url <- paste(
-        .BASE_URL, pipeline, paste0(pipeline, "_catalog.tsv"),
-        sep = "/"
-    ) |>
-        readr::read_tsv(show_col_types = FALSE)
+.CATALOG_COL_TYPES <- "ccccccccccccccccccccccddc"
+
+#' @rdname listFiles
+#'
+#' @description The `getCatalog` function retrieves a catalog of all available
+#'   HoVerNet and ProvGigaPath files, including filenames, sizes, pipelines
+#'   used, tumor types, and data levels.
+#'
+#' @param pipeline `character()` One or both "hovernet" and/or "provgigapath"
+#'   specifying which pipeline(s) to include in the catalog. Default includes
+#'   both.
+#'
+#' @param redownload `logical(1L)` Whether to redownload the catalog file even
+#'   if it is already cached locally. Default is `FALSE`.
+#'
+#' @returns `getCatalog`: A `tibble` containing the full catalog of available
+#'   files for the specified pipeline(s).
+#'
+#' @examplesIf interactive()
+#' ## Get the full catalog of available files
+#' getCatalog(pipeline = c("hovernet", "provgigapath"))
+#' @export
+getCatalog <-
+    function(pipeline = c("hovernet", "provgigapath"), redownload = FALSE)
+{
+    pipeline <- match.arg(pipeline, several.ok = TRUE)
+    catalog <- .download_catalog(redownload = redownload)
+    readr::read_tsv(catalog, col_types = .CATALOG_COL_TYPES) |>
+        subset(pipeline %in% pipeline)
+}
+
+#' @importFrom httr2 request req_headers req_perform resp_body_json
+.download_catalog <- function(redownload) {
+    resp <- request("https://zenodo.org/api/records/17981132") |>
+        req_headers(
+            Accept = "application/json"
+        ) |>
+        req_perform() |>
+        resp_body_json()
+
+    .cache_url_file(
+        resp$files[[1L]]$links$self, redownload = redownload
+    )
 }