refactor: tweak download and list functions (#5)

Merge branch 'master' into dev

# Conflicts:
#	R/main.R

DESCRIPTION

@@ -9,7 +9,7 @@ Description: Environmental ocean data modeled both for the present and for futur
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Suggests: 
     httr,
     testthat (>= 3.0.0)

NAMESPACE

@@ -1,3 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
-export(download_griddap_dataset)
+export(download_dataset)
+export(list_layers)

R/main.R

@@ -1,63 +1,9 @@
-.list_layers <- function(..., simplify = TRUE){
-
-  # Retrieve either full list of layers or loop-up by free-text search
-  if(missing(...)){
-    layers <- rerddap::ed_datasets(which = "griddap", url = erddap.bio_oracle.org())
-  }else{
-    layers <- rerddap::ed_search_adv(..., url = erddap.bio_oracle.org())
-    layers <- dplyr::bind_rows(layers$alldata)
-    attr(layers, "class")
-  }
-
-  # Aftermath
-  layers <- colnames_normalize(layers)
-  if(simplify) layers <- simplify(layers)
-
-  layers
-}
-
-colnames_normalize <- function(df){
-  colnames(df) <- df %>% colnames() %>% tolower()
-  colnames(df) <- gsub(".","_", colnames(df), fixed = TRUE)
-  df
-}
-
-simplify <- function(df){
-  cols_desired <- c("dataset_id", "title", "summary")
-  cols_desired_exist <- all(cols_desired %in% colnames(df))
-
-  if(cols_desired_exist){
-    df <- df[, cols_desired]
-  }
-
-  df
-}
-
-#' List the layers in the Bio-Oracle dataset
-#'
-#' @param ... Free text search or pass params to [rerddap::ed_search_adv]
-#'
-#' @return a data frame with the dataset ID that can be later passed to [download_layers]
-#' and further information
-#' @export
-#'
-#' @seealso [download_layers]
-#'
-#' @examples \dontrun{
-#' list_layers()
-#' list_layers("Ocean Temperature 2100")
-#' list_layers("thetao_ssp119_2020_2100_depthmean")
-#' }
-list_layers <- memoise::memoise(.list_layers)
-
-
-
 #' Downloads a griddap dataset from an ERDDAP server
 #'
 #' @param dataset
 #' @param variables
 #' @param constraints
-#' @param response
+#' @param fmt
 #' @param directory
 #' @param verbose
 #'
@@ -66,38 +12,51 @@ list_layers <- memoise::memoise(.list_layers)
 #'
 #' @seealso [list_layers]
 #'
-#' @examples
-#'
+#' @examples \dontrun{
 #' # Test variables
-#' dataset_id = "tas_baseline_2000_2020_depthsurf"
+#' datasetid = "tas_baseline_2000_2020_depthsurf"
 #' time = c('2001-01-01T00:00:00Z', '2010-01-01T00:00:00Z')
 #' latitude = c(10, 20)
 #' longitude = c(120, 130)
-#' variables = NULL
+#' variables = c("tas_max", "tas_min")
 #' constraints = list(time, latitude, longitude)
 #' names(constraints) = c("time", "latitude", "longitude")
 #'
 #' # Test call
-#' download_layers(dataset_id, variables, constraints, debug = TRUE, directory = "./cache/")
-download_layers = function(dataset, variables, constraints, response = "nc",
-                            directory = "./", verbose = TRUE, debug = FALSE) {
+#' download_dataset(datasetid, variables, constraints)
+#' }
+download_dataset = function(dataset,
+                                    variables,
+                                    constraints,
+                                    fmt="nc",
+                                    directory=FALSE,
+                                    verbose=TRUE,
+                                    debug=FALSE
+) {
+
+  printer = function(message, verbose=parent.frame()$verbose) {
+    if(verbose) { message(message) }
+  }
 
-  printer = function(message, verbose = parent.frame()$verbose) {
-    if(verbose) { message(message)}
+  if(fmt == "raster"){
+    is_raster <- TRUE
+    fmt <- "nc"
   }
+
   # Args to be passed to griddap call later on
   docallargs = list()
-  out = rerddap::info(datasetid = dataset, url = erddap.bio_oracle.org())
+  docallargs[["fmt"]] = fmt
+  out = rerddap::info(datasetid=dataset, url = erddap.bio_oracle.org())
   docallargs[["datasetx"]] = out
 
   printer(sprintf("Selected dataset %s.", dataset))
   printer(sprintf("Dataset info available at: %s/griddap/%s.html", out$base_url, dataset))
 
 
-  # Setting constraints that match TODO: raise warning if constraint does not exist
+  # Setting constraints that match
   for (constraint in names(constraints)) {
     if (constraint %in% names(out$alldata)) {
-      docallargs[[constraint]] = get(constraint, constraints)
+      docallargs[[constraint]]= get(constraint, constraints)
     }
   }
 
@@ -113,9 +72,12 @@ download_layers = function(dataset, variables, constraints, response = "nc",
   printer(sprintf("Selected %s variables: %s", length(valid_variables), toString(valid_variables)))
 
   # Set directory for storing data
-  cache_dir <- hoardr::hoard()
-  cache_dir$cache_path_set(full_path=directory)
-  docallargs[["store"]] = rerddap::disk(cache_dir$cache_path_get())
+
+  if (!isFALSE(directory)) {
+    cache_dir <- hoardr::hoard()
+    cache_dir$cache_path_set(full_path=directory)
+    docallargs[["store"]] = rerddap::disk(cache_dir$cache_path_get())
+  }
 
   # Debug flag to check args if needed
   if (debug) {
@@ -124,8 +86,66 @@ download_layers = function(dataset, variables, constraints, response = "nc",
 
   # Call
   res = do.call(rerddap::griddap, docallargs)
+
+  if(is_raster) res <- griddap_to_terra(res)
+
   return(res)
 }
 
+griddap_to_terra <- function(res){
+  terra::rast(x$summary$filename)
+}
+
+
+
+.list_layers <- function(..., simplify = TRUE){
+
+  # Retrieve either full list of layers or loop-up by free-text search
+  if(missing(...)){
+    layers <- rerddap::ed_datasets(which = "griddap", url = erddap.bio_oracle.org())
+  }else{
+    layers <- rerddap::ed_search_adv(..., url = erddap.bio_oracle.org())
+    layers <- dplyr::bind_rows(layers$alldata)
+    attr(layers, "class")
+  }
+
+  # Aftermath
+  layers <- colnames_normalize(layers)
+  if(simplify) layers <- simplify(layers)
+
+  layers
+}
+
+colnames_normalize <- function(df){
+  colnames(df) <- df %>% colnames() %>% tolower()
+  colnames(df) <- gsub(".","_", colnames(df), fixed = TRUE)
+  df
+}
+
+simplify <- function(df){
+  cols_desired <- c("dataset_id", "title", "summary")
+  cols_desired_exist <- all(cols_desired %in% colnames(df))
 
+  if(cols_desired_exist){
+    df <- df[, cols_desired]
+  }
 
+  df
+}
+
+#' List the layers in the Bio-Oracle dataset
+#'
+#' @param ... Free text search or pass params to [rerddap::ed_search_adv]
+#'
+#' @return a data frame with the dataset ID that can be later passed to [download_layers]
+#' and further information
+#' @export
+#'
+#' @seealso [download_layers]
+#'
+#' @examples \dontrun{
+#' list_layers()
+#' list_layers("Ocean Temperature 2100")
+#' list_layers("thetao_ssp119_2020_2100_depthmean")
+#' }
+list_layers <- memoise::memoise(.list_layers)