Merge pull request #129 from NIEHS/mm-modis-1007

1.1.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: amadeus
 Title: Accessing and Analyzing Large-Scale Environmental Data
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: c(
     person(given = "Mitchell", family = "Manware", role = c("aut", "ctb"), comment = c(ORCID = "0009-0003-6440-6106")),
     person(given = "Insang", family = "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")),

R/download.R

@@ -2279,7 +2279,7 @@ download_koppen_geiger <- function(
 #' @return
 #' * For \code{hash = FALSE}, NULL
 #' * For \code{hash = TRUE}, an \code{rlang::hash_file} character.
-#' * HDF (.hdf) files will be stored in
+#' * HDF (.hdf) files will be stored in year/day_of_year sub-directories within
 #' \code{directory_to_save}.
 #' @importFrom Rdpack reprompt
 #' @references
@@ -2493,17 +2493,27 @@ download_modis <- function(
       nasa_earth_data_token,
       "\" -O ",
       directory_to_save,
+      splitter,
       download_name,
       "\n"
     )
 
     #### filter commands to non-existing files
     download_command <- download_command[
       which(
-        !file.exists(paste0(directory_to_save, download_name))
+        !file.exists(paste0(directory_to_save, splitter, download_name))
       )
     ]
 
+    new_dirs <- unique(
+      sprintf("%s%s", directory_to_save, splitter)
+    )
+
+    lapply(
+      new_dirs,
+      function(x) dir.create(x, recursive = TRUE, showWarnings = FALSE)
+    )
+
     # avoid any possible errors by removing existing command files
     download_sink(commands_txt)
     #### cat command only if file does not already exist
@@ -2517,7 +2527,7 @@ download_modis <- function(
     )
 
     message("Requests were processed.\n")
-    return(NULL)
+    return(download_hash(hash, directory_to_save))
   }
 
 
@@ -2597,21 +2607,38 @@ download_modis <- function(
         filelist,
         value = TRUE
       )
-    download_url <- sprintf("%s%s", ladsurl, filelist_sub)
 
     download_name <- sapply(
-      strsplit(download_url, paste0("/", day, "/")), `[`, 2
+      strsplit(filelist_sub, paste0("/", day, "/")), `[`, 2
+    )
+
+    dir_str_julian <-
+      lapply(download_name, function(x) strsplit(x, ".A")[[1]][3])
+
+    dir_substr <- paste0(
+      substr(dir_str_julian, 1, 4), "/",
+      substr(dir_str_julian, 5, 7), "/"
+    )
+
+    new_dirs <- unique(
+      sprintf("%s%s", directory_to_save, dir_substr)
+    )
+
+    lapply(
+      new_dirs,
+      function(x) dir.create(x, recursive = TRUE, showWarnings = FALSE)
     )
 
     # Main wget run
     download_command <- paste0(
       "wget -e robots=off -np -R .html,.tmp ",
       "-nH --cut-dirs=3 \"",
-      download_url,
+      filelist_sub,
       "\" --header \"Authorization: Bearer ",
       nasa_earth_data_token,
       "\" -O ",
       directory_to_save,
+      dir_substr,
       download_name,
       "\n"
     )
@@ -2620,7 +2647,7 @@ download_modis <- function(
     download_command <- download_command[
       which(
         !file.exists(
-          paste0(directory_to_save, download_name)
+          paste0(directory_to_save, dir_substr, download_name)
         )
       )
     ]

tests/testthat/test-terraclimate.R

@@ -44,7 +44,7 @@ testthat::test_that("download_terraclimate (single year)", {
   # function parameters
   year <- 2019
   variables <- "Precipitation"
-  directory_to_save <- paste0(tempdir(), "/terracclimate/")
+  directory_to_save <- paste0(tempdir(), "/terraclimate/")
   # run download function
   download_data(dataset_name = "terraclimate",
                 year = year,