From 88c4e277db516dcb1f8e2809a626d95f01e78327 Mon Sep 17 00:00:00 2001
From: "Azadpour, Elmera" <eazadpour@usgs.gov>
Date: Thu, 3 Oct 2024 11:58:20 -0700
Subject: [PATCH] edit fetch utils function
---
1_fetch/src/fetch_utils.R | 109 ++++++++++++++++++++++++++++++++------
1 file changed, 93 insertions(+), 16 deletions(-)
diff --git a/1_fetch/src/fetch_utils.R b/1_fetch/src/fetch_utils.R
index fc3b829..b02e57d 100644
--- a/1_fetch/src/fetch_utils.R
+++ b/1_fetch/src/fetch_utils.R
@@ -1,16 +1,93 @@
-#' @title Download file from ScienceBase
-#' @description Download a file from ScienceBase and save it to a specified
-#' directory
-#' @param sb_id id for ScienceBase data release
-#' @param filename filename of item in data release
-#' @param dest_dir directory to which to download the file
-#' @return the filepath of the saved file
-download_from_sb <- function(sb_id, filename, dest_dir) {
- filepath <- file.path(dest_dir, filename)
-
- sbtools::item_file_download(sb_id = sb_id,
- names = filename,
- destinations = filepath)
-
- return(filepath)
-}
\ No newline at end of file
+#' Initialize ScienceBase session and download files
+#'
+#' @param sb_id chr; ScienceBase ID
+#' @param names chr; names of files to download from ScienceBase
+#' @param destinations chr; write path location for downloaded files
+#' @param renviron_file chr; path to .Renviron file where credentials are cached
+#' @param ... additional arguments passed to `sbtools::item_file_download()`
+#'
+#' @return chr; path to downloaded files
+#'
+sb_initialize_and_download <- function(sb_id, names, destinations,
+ renviron_file = ".Renviron", ...) {
+ # Initialize ScienceBase session
+ sb_login_cached(renviron_file = renviron_file)
+
+ # Download SB files
+ sbtools::item_file_download(
+ sb_id = sb_id,
+ names = names,
+ destinations = destinations,
+ ...
+ )
+
+ return(destinations)
+}
+
+#' Login to ScienceBase using cached credentials
+#'
+#' @param renviron_file chr; path to .Renviron file
+#'
+#' @return `TRUE` if logged in. Error if not.
+#'
+sb_login_cached <- function(renviron_file) {
+ # If logged in, return TRUE and skip the rest
+ if (sbtools::is_logged_in()) {
+ return(TRUE)
+ }
+
+ # Try a token refresh
+ tryCatch(
+ sbtools:::token_refresh(),
+ warning = function(x) {},
+ error = function(x) FALSE
+ )
+
+ if (sbtools::is_logged_in()) {
+ return(TRUE)
+ }
+
+ # If .Renviron file does not exist, re-initialize
+ if (!file.exists(renviron_file)) {
+ cli::cli_abort(c(
+ "Could not find the specified file: {.file {renviron_file}}.",
+ "i" = "Follow the instructions in {.file README.md} to initalize and cache
+ ScienceBase login credentials."
+ ))
+ }
+
+ # Read .Renviron file
+ existing <- readLines(renviron_file)
+ sb_token_idx <- which(startsWith(existing, "sb_token="))
+ sb_username_idx <- which(startsWith(existing, "sb_username="))
+
+ # If SB credentials not found, throw error
+ if (any(length(sb_token_idx) == 0, length(sb_username_idx) == 0)) {
+ cli::cli_abort(c(
+ "Could not find the username or token in the specified file:
+ {.file {renviron_file}}.",
+ "i" = "Follow the instructions in {.file README.md} to re-initalize and
+ cache ScienceBase login credentials."
+ ))
+ }
+
+ # Get ScienceBase credentials
+ sb_token <- stringr::str_remove(existing[sb_token_idx], "^sb_token=")
+ sb_username <- stringr::str_remove(existing[sb_username_idx], "^sb_username=")
+
+ # Initialize ScienceBase session with cached credentials
+ sbtools::initialize_sciencebase_session(
+ username = sb_username,
+ token_text = sb_token
+ )
+
+ if (sbtools::is_logged_in()) {
+ return(TRUE)
+ } else {
+ cli::cli_abort(c(
+ "Could not login to ScienceBase using cached credentials.",
+ "i" = "Follow the instructions in {.file README.md} to re-initalize and
+ cache ScienceBase login credentials."
+ ))
+ }
+}
--
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