Merge pull request #8 from vinisalazar/dev

Merge 'dev' into 'main'

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: 7.2.0
 Suggests: 
     httr,
     testthat (>= 3.0.0)

NAMESPACE

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

R/draft.R → R/main.R

@@ -1,10 +1,10 @@
 #' Downloads a griddap dataset from an ERDDAP server
 #'
-#' @param erddap_server
+#' @param url
 #' @param dataset
 #' @param variables
 #' @param constraints
-#' @param response
+#' @param fmt
 #' @param directory
 #' @param verbose
 #'
@@ -21,15 +21,16 @@
 #' longitude = c(120, 130)
 #' variables = c("o2_mean")
 #' constraints = list(time, latitude, longitude)
+#' fmt = "nc"
 #' names(constraints) = c("time", "latitude", "longitude")
 #' # Test call
-#' download_griddap_dataset(url, datasetid, variables, constraints)
-download_griddap_dataset = function(erddap_server,
-                                    dataset,
+#' download_dataset(datasetid, variables, constraints)
+download_dataset = function(dataset,
                                     variables,
                                     constraints,
-                                    response="nc",
-                                    directory="./",
+                                    url="https://erddap-test.emodnet.eu/erddap/",
+                                    fmt="nc",
+                                    directory=FALSE,
                                     verbose=TRUE,
                                     debug=FALSE
 ) {
@@ -39,7 +40,8 @@ download_griddap_dataset = function(erddap_server,
   }
   # Args to be passed to griddap call later on
   docallargs = list()
-  out = rerddap::info(datasetid=dataset, url=erddap_server)
+  docallargs[["fmt"]] = fmt
+  out = rerddap::info(datasetid=dataset, url=url)
   docallargs[["x"]] = out
 
   printer(sprintf("Selected dataset %s.", dataset))
@@ -65,9 +67,12 @@ download_griddap_dataset = function(erddap_server,
   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) {
@@ -80,3 +85,11 @@ download_griddap_dataset = function(erddap_server,
   return(res)
 }
 
+
+list_layers = function(url = "https://erddap-test.emodnet.eu/erddap/", filter_biooracle=TRUE) {
+  response = rerddap::ed_datasets("griddap", url=url)
+  if (isTRUE(filter_biooracle)) {
+    response = response %>% filter(grepl("biooracle",Dataset.ID))
+  }
+  return(response)
+}

tests/testthat/test-download.R

@@ -15,16 +15,20 @@ test_that("download dataset works", {
   # Test call
   server_is_working <- httr::status_code(httr::HEAD(url)) == 200
   if(server_is_working){
-    test <- download_griddap_dataset(url, datasetid, variables, constraints)
+    test <- download_dataset(datasetid, variables, constraints, url, fmt="csv")
 
     expect_type(test, "list")
-    expect_s3_class(test, "griddap_nc")
-    expect_s3_class(test$data, "data.frame")
+    expect_s3_class(test, "griddap_csv")
+    expect_s3_class(test, "data.frame")
 
-    # Test download to custom dir
+    # Test download to custom dir, and csv response
     temp_dir <- normalizePath(tempdir())
-    test_dir <- download_griddap_dataset(directory = temp_dir, url, datasetid, variables, constraints)
+    test_dir <- download_dataset(datasetid, variables, constraints, url, fmt="nc", directory = temp_dir)
+    expect_s3_class(test_dir, "griddap_nc")
+    expect_s3_class(test_dir$data, "data.frame")
 
+    print(test_dir$summary$filename)
+    print(dirname(test_dir$summary$filename))
     out_dir <- normalizePath(dirname(test_dir$summary$filename))
     expect_equal(out_dir, temp_dir)
   }