From 9a9a40f6212c983fda50cea08f51a379d1458152 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Thu, 15 Jun 2023 15:53:53 +0200
Subject: [PATCH 1/2] fix broken URL

---
 inst/doc/usecase.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/doc/usecase.md b/inst/doc/usecase.md
index 47ee89e..80614d0 100644
--- a/inst/doc/usecase.md
+++ b/inst/doc/usecase.md
@@ -78,7 +78,7 @@ The problem may occur when the dimension number of the splitted selector is more
 
    4. [Use two functions in workflow](inst/doc/usecase/ex2_4_two_func.R)  
 
-   5. [RainFARM precipitation downscaling](https://earth.bsc.es/gitlab/es/startR/-/blob/develop-RainFARMCase/inst/doc/usecase/ex2_5_rainFARM.R)  
+   5. [RainFARM precipitation downscaling](/inst/doc/usecase/ex2_5_rainFARM.R)  
       This example shows how to apply a statistical downscaling function with startR and simultaneously (considering the memory size if unnecessary dimensions are included) saves the data by chunks (e.g., chunking those dimensions which are not required for downscaling) in the esarchive format. It is not recommended to save big outputs. Consider to perform some analysis and then retrieve the result instead of saving data. This is a simplified example of RainFARM for more information visit: https://www.medscope-project.eu/products/data/. 
 Find more explanation of this use case in FAQ [How-to-27](inst/doc/faq.md#27-utilize-chunk-number-in-the-function).
 
-- 
GitLab


From ddf51ba036eec8126b46537eb9010c7c16cdb213 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Thu, 15 Jun 2023 23:23:12 +0200
Subject: [PATCH 2/2] return variable metadata when retrieve = F

---
 R/Start.R                                     | 119 +++-
 R/zzz.R                                       |   5 +-
 tests/testthat/test-Start-metadata_dims.R     | 542 +++++++++++++++++-
 .../testthat/test-Start-metadata_reshaping.R  |   2 +-
 4 files changed, 620 insertions(+), 48 deletions(-)

diff --git a/R/Start.R b/R/Start.R
index 702b776..92eb16d 100644
--- a/R/Start.R
+++ b/R/Start.R
@@ -4108,7 +4108,90 @@ Start <- function(..., # dim = indices/selectors,
         }
       }
     }
+    # Retrieve variable metadata
+    # Compare array_of_metadata_flags with array_of_files_to_load to know which files to take for metadata
+    if (!is.null(metadata_dims)) {
+      array_of_metadata_flags <- array(FALSE, dim = dim(array_of_files_to_load))
+      metadata_indices_to_load <- as.list(rep(1, length(dim(array_of_files_to_load))))
+      names(metadata_indices_to_load) <- names(dim(array_of_files_to_load))
+      metadata_indices_to_load[metadata_dims] <- as.list(rep(TRUE, length(metadata_dims)))
+      array_of_metadata_flags <- do.call('[<-', c(list(array_of_metadata_flags),  metadata_indices_to_load,
+                                                  list(value = rep(TRUE, prod(dim(array_of_files_to_load)[metadata_dims])))))
+
+      if (tail(names(dim(array_of_files_to_load)), 1) != found_pattern_dim) {
+        tmp1 <- s2dv::Reorder(array_of_files_to_load, c(2:length(dim(array_of_files_to_load)), 1))
+        tmp2 <- s2dv::Reorder(array_of_metadata_flags, c(2:length(dim(array_of_metadata_flags)), 1))
+        files_for_metadata <- tmp1[tmp2]
+      } else {
+        files_for_metadata <- array_of_files_to_load[array_of_metadata_flags]
+      }
 
+      # Get variable name
+      #NOTE: This part probably will fail when one netCDF file has more than one variable.
+      if (found_pattern_dim %in% metadata_dims) {  # metadata_dims has "dat"
+        if (any(metadata_dims %in% c('var', 'variable'))) { # metadata_dim is c('dat', 'var')
+          how_many_vars <-  length(dat[[1]][['selectors']]$var[[1]])
+        } else if (length(metadata_dims) > 1) {  # metadata_dims is c('dat', xxx)
+          how_many_vars <- length(dat[[1]][['selectors']][[metadata_dims[which(found_pattern_dim != metadata_dims)]]][[1]])
+        } else {  # metadata_dims is 'dat'
+          how_many_vars <- 1
+        }
+        tmp_var <- matrix(NA, how_many_vars, length(dat))
+        for (i_dat in 1:dim(array_of_metadata_flags)[found_pattern_dim]) {
+          if (any(metadata_dims %in% c('var', 'variable'))) { # metadata_dims has "var"
+            tmp_var[, i_dat] <- dat[[i_dat]][['selectors']]$var[[1]]
+          } else if (length(metadata_dims) > 1) {  # metadata_dims is c('dat', xxx)
+            tmp_var[, i_dat] <- rep(dat[[i_dat]][['selectors']]$var[[1]][1],
+                                    length(dat[[1]][['selectors']][[metadata_dims[which(found_pattern_dim != metadata_dims)]]][[1]]))
+          } else {  # metadata_dims is 'dat'
+            tmp_var[, i_dat] <- dat[[i_dat]][['selectors']]$var[[1]][1]
+          }
+        }
+
+        # if metadat_dims = c('dat', 'var') and [dat = 2, var = 2], tmp_var has length 4, like c('tas', 'tos', 'tas', 'tos').
+        # if metadata_dims = 'dat' and [dat = 2], tmp_var has length 2 like c('tas', 'tos').
+        tmp_var <- c(tmp_var)
+
+      } else {  # metadata_dims doesn't have "dat"
+        if (any(metadata_dims %in% c('var', 'variable'))) { # metadata_dims has "var"
+          tmp_var <- dat[[1]][['selectors']]$var[[1]]
+        } else {
+          tmp_var <- rep(dat[[1]][['selectors']]$var[[1]][1], length(dat[[1]][['selectors']][[metadata_dims]][[1]]))
+        }
+        # if metadata_dims = 'var' and [var = 2], tmp_var has length 2 like c('tas', 'tos')
+        # if metadata_dims = 'table' and [table = 2], tmp_var has length 1 like 'tas'
+      }
+
+      loaded_metadata <- vector('list', length = length(files_for_metadata))
+      for (i_file in 1:length(files_for_metadata)) {
+        #NOTE: Not use ncatt_get() because it only gets the attr shown with ncdump -h
+        tmp <- file_opener(files_for_metadata[i_file])
+        if (!is.null(tmp)) {  # if file exists
+          loaded_metadata[[i_file]][[1]] <- tmp$var[[tmp_var[i_file]]]
+          names(loaded_metadata[[i_file]]) <- tmp_var[i_file]
+          file_closer(tmp)
+        }
+      }
+      # Find loaded_metadata_files identical as "retrieve = T" case. If dataset_has_files is F, deduct that dataset from counting
+      ind_loaded_metadata_has_values <- which(!sapply(loaded_metadata, is.null)) # c(1, 2, 4)
+      if (!all(dataset_has_files)) {  # If dataset_has_files has F, deduct that dataset from counting
+        if (found_pattern_dim %in% metadata_dims) {  # metadata_dims has "dat" 
+          dataset_has_files_expand <- rep(dataset_has_files, each = how_many_vars)
+          i_ind <- 1
+          while (i_ind <= length(ind_loaded_metadata_has_values)) { # 3, 4, 8
+            if (ind_loaded_metadata_has_values[i_ind] > i_ind) {
+              ind_loaded_metadata_has_values[i_ind] <- ind_loaded_metadata_has_values[i_ind] - length(which(!dataset_has_files_expand[1:dataset_has_files_expand[i_ind]]))
+            }
+            i_ind <- i_ind + 1
+          }
+        }
+      }
+      loaded_metadata_files <- as.character(ind_loaded_metadata_has_values)
+      loaded_metadata <- loaded_metadata[which(!sapply(loaded_metadata, is.null))]
+      return_metadata <- create_metadata_list(array_of_metadata_flags, metadata_dims, pattern_dims,
+                                              loaded_metadata_files, loaded_metadata, dat_names,
+                                              dataset_has_files)
+    }
   }
   # Print the warnings from transform
   if (!is.null(c(warnings1, warnings2, warnings3))) {
@@ -4150,27 +4233,28 @@ Start <- function(..., # dim = indices/selectors,
     file_selectors[[dat[[i]][['name']]]] <- dat[[i]][['selectors']][which(names(dat[[i]][['selectors']]) %in% found_file_dims[[i]])]
   }
 
+  # Prepare attr Variables
+  if (all(sapply(return_metadata, is.null))) {
+    # We don't have metadata of the variable (e.g., tas). The returned metadata list only 
+    # contains those are specified in argument "return_vars".
+    Variables_list <- c(list(common = picked_common_vars), picked_vars)
+    .warning(paste0("Metadata cannot be retrieved. The reason may be the ",
+                    "non-existence of the first file. Use parameter 'metadata_dims'",
+                    " to assign to file dimensions along which to return metadata, ",
+                    "or check the existence of the first file."))
+  } else {
+    # Add the metadata of the variable (e.g., tas) into the list of picked_vars or
+    # picked_common_vars.
+    Variables_list <- combine_metadata_picked_vars(
+                        return_metadata, picked_vars, picked_common_vars,
+                        metadata_dims, pattern_dims, length(dat))
+  }
+
   if (retrieve) {
     if (!silent) {
       .message("Successfully retrieved data.")
     }
 
-    if (all(sapply(return_metadata, is.null))) {
-      # We don't have metadata of the variable (e.g., tas). The returned metadata list only 
-      # contains those are specified in argument "return_vars".
-      Variables_list <- c(list(common = picked_common_vars), picked_vars)
-      .warning(paste0("Metadata cannot be retrieved. The reason may be the ",
-                      "non-existence of the first file. Use parameter 'metadata_dims'",
-                      " to assign to file dimensions along which to return metadata, ",
-                      "or check the existence of the first file."))
-    } else {
-      # Add the metadata of the variable (e.g., tas) into the list of picked_vars or
-      # picked_common_vars.
-      Variables_list <- combine_metadata_picked_vars(
-                          return_metadata, picked_vars, picked_common_vars,
-                          metadata_dims, pattern_dims, length(dat))
-    }
-
     attributes(data_array) <- c(attributes(data_array), 
                                 list(Variables = Variables_list,
                                      Files = array_of_files_to_load, 
@@ -4200,7 +4284,7 @@ Start <- function(..., # dim = indices/selectors,
     start_call[['retrieve']] <- TRUE
     attributes(start_call) <- c(attributes(start_call),
                                 list(Dimensions = final_dims_fake,
-                                     Variables = c(list(common = picked_common_vars), picked_vars),
+                                     Variables = Variables_list,
                                      ExpectedFiles = array_of_files_to_load,
                                      FileSelectors = file_selectors,
                                      PatternDim = found_pattern_dim,
@@ -4237,6 +4321,7 @@ Start <- function(..., # dim = indices/selectors,
   second_round_indices <- work_piece[['second_round_indices']]
   #print("2")
   file_to_open <- work_piece[['file_path']]
+  # Get data and metadata
   sub_array <- file_data_reader(file_to_open, NULL, 
                                 work_piece[['file_selectors']],
                                 first_round_indices, synonims)
diff --git a/R/zzz.R b/R/zzz.R
index 22805ff..1e56e29 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1363,7 +1363,10 @@ combine_metadata_picked_vars <- function(return_metadata, picked_vars, picked_co
       sublist_names <- lapply(return_metadata, names)[[kk]]
       if (!is.null(sublist_names)) {
         for (jj in 1:length(sublist_names)) {
-          picked_vars[[kk]][[sublist_names[jj]]] <- return_metadata[[kk]][[jj]]
+          if (!is.null(return_metadata[[kk]][[jj]])) {
+            picked_vars[[kk]] <- c(picked_vars[[kk]], list(return_metadata[[kk]][[jj]]))
+            names(picked_vars[[kk]])[length(picked_vars[[kk]])] <- names(return_metadata[[kk]][jj])
+          }
         }
       }
     }
diff --git a/tests/testthat/test-Start-metadata_dims.R b/tests/testthat/test-Start-metadata_dims.R
index ce30eec..4251c71 100644
--- a/tests/testthat/test-Start-metadata_dims.R
+++ b/tests/testthat/test-Start-metadata_dims.R
@@ -19,10 +19,6 @@ suppressWarnings(
                 retrieve = T
                )
 )
-  expect_equal(
-  length(attr(data, 'Variables')),
-  2
-  )
   expect_equal(
   names(attr(data, 'Variables')),
   c("common", "system5_m1")
@@ -45,6 +41,41 @@ suppressWarnings(
   tolerance = 0.0001
   )
 
+
+suppressWarnings(
+  dataF <- Start(dat = list(list(name = 'system5_m1', path = repos)),
+                var = 'tas',
+                sdate = '20170101',
+                ensemble = indices(1),
+                time = indices(1),
+                lat = indices(1:2),
+                lon = indices(2:3),
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                return_vars = list(time = 'sdate',
+                                   lon = 'dat',
+                                   lat = 'dat'),
+                metadata_dims = 'dat',  # it can be omitted since it is automatically specified as 'dat'
+                retrieve = F
+               )
+)
+  expect_equal(
+  names(attr(dataF, 'Variables')),
+  c("common", "system5_m1")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$common),
+  c('time', 'tas')
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system5_m1),
+  c("lon", "lat")
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$common$tas),
+  22
+  )
+
 })
 
 
@@ -69,10 +100,6 @@ suppressWarnings(
                 retrieve = T
                )
 )
-  expect_equal(
-  length(attr(data, 'Variables')),
-  3
-  )
   expect_equal(
   names(attr(data, 'Variables')),
   c("common", "system4_m1", "system5_m1")
@@ -107,6 +134,52 @@ suppressWarnings(
   c(247.2570, 248.5016),
   tolerance = 0.0001
   )
+
+suppressWarnings(
+  dataF <- Start(dat = list(list(name = 'system4_m1', path = repos2),
+                           list(name = 'system5_m1', path = repos)),
+                var = 'tas',
+                sdate = '20170101',
+                ensemble = indices(1),
+                time = indices(1),
+                lat = indices(1:2),
+                lon = indices(2:3),
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                return_vars = list(time = 'sdate',
+                                   lon = 'dat',
+                                   lat = 'dat'),
+                metadata_dims = 'dat',  # it can be omitted since it is automatically specified as 'dat'
+                retrieve = F
+               )
+)
+
+  expect_equal(
+  names(attr(dataF, 'Variables')),
+  c("common", "system4_m1", "system5_m1")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$common),
+  'time'
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system4_m1),
+  c("lon", "lat", "tas")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system5_m1),
+  c("lon", "lat", "tas")
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system5_m1$tas),
+  22
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system4_m1$tas),
+  22
+  )
+
+
 })
 
 test_that("3. One data set, two vars", {
@@ -127,10 +200,6 @@ suppressWarnings(
                 retrieve = TRUE
                )
 )
-  expect_equal(
-  length(attr(data, 'Variables')),
-  2
-  )
   expect_equal(
   names(attr(data, 'Variables')),
   c("common", "dat1")
@@ -161,6 +230,43 @@ suppressWarnings(
   c(250.00110, 25.04345),
   tolerance = 0.0001
   )
+
+
+suppressWarnings(
+  dataF <- Start(dat = repos,
+                var = var,
+                time = indices(1),
+                lat = indices(9:10),
+                lon = indices(10:11),
+                return_vars = list(lat = NULL, lon = NULL),
+                metadata_dims = 'var',
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                retrieve = F
+               )
+)
+
+  expect_equal(
+  names(attr(dataF, 'Variables')),
+  c("common", "dat1")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$common),
+  c('lat', 'lon', 'tas', 'clt')
+  )
+  expect_equal(
+  is.null(attr(dataF, 'Variables')$dat1),
+  TRUE
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$common$tas),
+  22
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$common$clt),
+  22
+  )
+
 })
 
 test_that("4. Two data sets, two vars", {
@@ -184,10 +290,6 @@ suppressWarnings(
                 retrieve = T
                )
 )
-  expect_equal(
-  length(attr(data, 'Variables')),
-  3
-  )
   expect_equal(
   names(attr(data, 'Variables')),
   c("common", "system4_m1", "system5_m1")
@@ -213,6 +315,14 @@ suppressWarnings(
   11
   )
   expect_equal(
+  attr(data, 'Variables')$system4_m1$tas$dim[[1]][1:2],
+  list(name = 'longitude', len = 512)
+  )
+  expect_equal(
+  attr(data, 'Variables')$system5_m1$tas$dim[[1]][1:2],
+  list(name = 'longitude', len = 1296)
+  )
+  expect_equal(
   data[1, , 1, 1, 1, 2, 2],
   c(247.227219, 6.370782),
   tolerance = 0.0001
@@ -223,6 +333,57 @@ suppressWarnings(
   tolerance = 0.0001
   )
 
+suppressWarnings(
+  dataF <- Start(dat = list(list(name = 'system4_m1', path = repos2),
+                           list(name = 'system5_m1', path = repos)),
+                var = c('tas', 'sfcWind'),
+                sdate = '20170101',
+                ensemble = indices(1),
+                time = indices(1),
+                lat = indices(1:2),
+                lon = indices(1:2),
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                return_vars = list(time = 'sdate',
+                                   lon = 'dat',
+                                   lat = 'dat'),
+                metadata_dims = 'dat',
+                retrieve = F
+               )
+)
+  expect_equal(
+  names(attr(dataF, 'Variables')),
+  c("common", "system4_m1", "system5_m1")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$common),
+  'time'
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system4_m1),
+  c("lon", "lat", "tas")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system5_m1),
+  c("lon", "lat", "tas")
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system5_m1$tas),
+  22
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system4_m1$tas),
+  22
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system4_m1$tas$dim[[1]][1:2],
+  list(name = 'longitude', len = 512)
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system5_m1$tas$dim[[1]][1:2],
+  list(name = 'longitude', len = 1296)
+  )
+
 #-------------------------------------------------------------
 suppressWarnings(
   data <- Start(dat = list(list(name = 'system4_m1', path = repos2),
@@ -243,10 +404,6 @@ suppressWarnings(
                )
 )
 
-  expect_equal(
-  length(attr(data, 'Variables')),
-  3
-  )
   expect_equal(
   names(attr(data, 'Variables')),
   c("common", "system4_m1", "system5_m1")
@@ -289,6 +446,83 @@ suppressWarnings(
   c(248.781540, 5.794801),
   tolerance = 0.0001
   )
+
+suppressWarnings(
+  dataF <- Start(dat = list(list(name = 'system4_m1', path = repos2),
+                           list(name = 'system5_m1', path = repos)),
+                var = c('tas', 'sfcWind'),
+                sdate = '20170101',
+                ensemble = indices(1),
+                time = indices(1),
+                lat = indices(1:2),
+                lon = indices(1:2),
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                return_vars = list(time = 'sdate',
+                                   lon = 'dat',
+                                   lat = 'dat'),
+                metadata_dims = c('dat', 'var'),
+                retrieve = F
+               )
+)
+
+  expect_equal(
+  names(attr(dataF, 'Variables')),
+  c("common", "system4_m1", "system5_m1")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$common),
+  'time'
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system4_m1),
+  c("lon", "lat", "tas", "sfcWind")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system5_m1),
+  c("lon", "lat", "tas", "sfcWind")
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system5_m1$tas),
+  22
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system5_m1$sfcWind),
+  22
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system4_m1$tas),
+  22
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system4_m1$sfcWind),
+  22
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system4_m1$tas$dim[[1]][1:2],
+  list(name = 'longitude', len = 512)
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system5_m1$tas$dim[[1]][1:2],
+  list(name = 'longitude', len = 1296)
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system4_m1$sfcWind$dim[[1]][1:2],
+  list(name = 'longitude', len = 512)
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system5_m1$sfcWind$dim[[1]][1:2],
+  list(name = 'lon', len = 1296)
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system4_m1$tas$name,
+  'tas'
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system5_m1$sfcWind$name,
+  'sfcWind'
+  )
+
 })
 
 test_that("5. Specify metadata_dims with another file dimension", {
@@ -313,10 +547,6 @@ suppressWarnings(
                )
 )
 
-  expect_equal(
-  length(attr(data, 'Variables')),
-  3
-  )
   expect_equal(
   names(attr(data, 'Variables')),
   c("common", "system4_m1", "system5_m1")
@@ -337,7 +567,167 @@ suppressWarnings(
   length(attr(data, 'Variables')$common$tas),
   12
   )
+  expect_equal(
+  attr(data, 'Variables')$common[[3]]$dim[[4]]$units,
+  "hours since 2016-01-01 00:00:00"
+  )
+
+suppressWarnings(
+  dataF <- Start(dat = list(list(name = 'system4_m1', path = repos2),
+                           list(name = 'system5_m1', path = repos)),
+                var = c('tas', 'sfcWind'),
+                sdate = c('20150101', '20160101', '20170101'),
+                ensemble = indices(1),
+                time = indices(1),
+                lat = indices(1:10),
+                lon = indices(1:10),
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                return_vars = list(time = 'sdate',
+                                   lon = 'dat',
+                                   lat = 'dat'),
+                metadata_dims = 'sdate',
+                retrieve = F
+               )
+)
+
+  expect_equal(
+  names(attr(dataF, 'Variables')),
+  c("common", "system4_m1", "system5_m1")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$common),
+  c('time', 'tas', 'tas', 'tas')
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system4_m1),
+  c("lon", "lat")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system5_m1),
+  c("lon", "lat")
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$common[[2]]),
+  22
+  )
+  expect_equal(
+  attr(data, 'Variables')$common$time,
+  attr(dataF, 'Variables')$common$time
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$common[[3]]$dim[[4]]$units,
+  "hours since 2016-01-01 00:00:00"
+  )
+
+#------------------------------------------------------------------
+suppressWarnings(
+  data <- Start(dat = list(list(name = 'system4_m1', path = repos2),
+                           list(name = 'system5_m1', path = repos)),
+                var = c('tas', 'sfcWind'),
+                sdate = c('20150101', '20160101', '20170101'),
+                ensemble = indices(1),
+                time = indices(1),
+                lat = indices(1:10),
+                lon = indices(1:10),
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                return_vars = list(time = 'sdate',
+                                   lon = 'dat',
+                                   lat = 'dat'),
+                metadata_dims = c('dat', 'sdate'),
+                retrieve = T
+               )
+)
+
+  expect_equal(
+  names(attr(data, 'Variables')),
+  c("common", "system4_m1", "system5_m1")
+  )
+  expect_equal(
+  names(attr(data, 'Variables')$common),
+  c('time')
+  )
+  expect_equal(
+  names(attr(data, 'Variables')$system4_m1),
+  c("lon", "lat", "tas", "tas", "tas")
+  )
+  expect_equal(
+  names(attr(data, 'Variables')$system5_m1),
+  c("lon", "lat", "tas", "tas", "tas")
+  )
+  expect_equal(
+  length(attr(data, 'Variables')$system4_m1[[3]]),
+  12
+  )
+  expect_equal(
+  length(attr(data, 'Variables')$system4_m1[[4]]),
+  12
+  )
+  expect_equal(
+  length(attr(data, 'Variables')$system5_m1[[5]]),
+  12
+  )
+  expect_equal(
+  attr(data, 'Variables')$system4_m1[[3]]$dim[[4]]$units,
+  "hours since 2015-01-01 00:00:00"
+  )
+  expect_equal(
+  attr(data, 'Variables')$system5_m1[[4]]$dim[[4]]$units,
+  "hours since 2016-01-01 00:00:00"
+  )
 
+suppressWarnings(
+  dataF <- Start(dat = list(list(name = 'system4_m1', path = repos2),
+                           list(name = 'system5_m1', path = repos)),
+                var = c('tas', 'sfcWind'),
+                sdate = c('20150101', '20160101', '20170101'),
+                ensemble = indices(1),
+                time = indices(1),
+                lat = indices(1:10),
+                lon = indices(1:10),
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                return_vars = list(time = 'sdate',
+                                   lon = 'dat',
+                                   lat = 'dat'),
+                metadata_dims = c('dat', 'sdate'),
+                retrieve = F
+               )
+)
+
+  expect_equal(
+  names(attr(dataF, 'Variables')),
+  c("common", "system4_m1", "system5_m1")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$common),
+  c('time')
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system4_m1),
+  c("lon", "lat", "tas", "tas", "tas")
+  )
+  expect_equal(
+  names(attr(dataF, 'Variables')$system5_m1),
+  c("lon", "lat", "tas", "tas", "tas")
+  )
+  expect_equal(
+  length(attr(dataF, 'Variables')$system4_m1[[3]]),
+  22
+  )
+  expect_equal(
+  attr(data, 'Variables')$common$time,
+  attr(dataF, 'Variables')$common$time
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system4_m1[[3]]$dim[[4]]$units,
+  "hours since 2015-01-01 00:00:00"
+  )
+  expect_equal(
+  attr(dataF, 'Variables')$system5_m1[[4]]$dim[[4]]$units,
+  "hours since 2016-01-01 00:00:00"
+  )
 })
 
 
@@ -374,6 +764,18 @@ data <- Start(repos = mask_path,
   length(attr(data, 'Variables')$common$nav_lat),
   8
   )
+#NOTE: The following code doesn't work, and since this netCDF file doesn't follow the convention (one var per file), we leave this development to the future.
+#suppressWarnings(
+#dataF <- Start(repos = mask_path,
+#              var = c('nav_lon', 'nav_lat'),
+#              t = 'first',
+#              z = 'first',
+#              x = 'all',
+#              y = 'all',
+#              return_vars = list(var_names = NULL),
+#              var_var = 'var_names',
+#              retrieve = F)
+#)
 
 })
 
@@ -396,7 +798,7 @@ suppressWarnings(
                 return_vars = list(time = 'sdate',
                                    lon = 'dat',
                                    lat = 'dat'),
-                metadata_dims = 'dat',  # it can be omitted since it is automatically specified as 'dat'
+                metadata_dims = 'dat', 
                 retrieve = T
                )
 )
@@ -409,6 +811,10 @@ suppressWarnings(
   list(lon = NULL, lat = NULL)
   )
   expect_equal(
+  names(attr(data, "Variables")$system5_m1),
+  c('lon', 'lat', 'tas')
+  )
+  expect_equal(
   length(attr(data, "Variables")$system5_m1$lon),
   1296
   )
@@ -421,6 +827,49 @@ suppressWarnings(
   array(c(NA, "/esarchive/exp/ecmwf/system5_m1/monthly_mean/tas_f6h/tas_20170101.nc"),
         dim = c(dat = 2, var = 1, sdate = 1))
   )
+
+suppressWarnings(
+ dataF <- Start(dat = list(list(name = 'system4_m1', path = repos2),
+                           list(name = 'system5_m1', path = repos)),
+                var = var,
+                sdate = '20170101',
+                ensemble = indices(1),
+                time = indices(1),
+                lat = 'all',
+                lon = 'all',
+                synonims = list(lat = c('lat', 'latitude'),
+                                lon = c('lon', 'longitude')),
+                return_vars = list(time = 'sdate',
+                                   lon = 'dat',
+                                   lat = 'dat'),
+                metadata_dims = 'dat', 
+                retrieve = F
+               )
+)
+
+  expect_equal(
+  attr(dataF, "Variables")$system4_m1,
+  list(lon = NULL, lat = NULL)
+  )
+  expect_equal(
+  length(attr(dataF, "Variables")$system5_m1$lon),
+  1296
+  )
+  expect_equal(
+  names(attr(dataF, "Variables")$system5_m1),
+  c('lon', 'lat', 'tas')
+  )
+  expect_equal(
+  length(attr(dataF, "Variables")$system5_m1$tas),
+  22
+  )
+  expect_equal(
+  attr(dataF, 'ExpectedFiles'),
+  array(c("/esarchive/exp/ecmwf/system4_m1/monthly_mean/tas_f2h/tas_20170101.nc", "/esarchive/exp/ecmwf/system5_m1/monthly_mean/tas_f6h/tas_20170101.nc"),
+        dim = c(dat = 2, var = 1, sdate = 1))
+  )
+
+
 })
 
 test_that("8. Two data sets, both have files but the first file is missing", {
@@ -457,10 +906,6 @@ data <- Start(dataset = path_list,
   5500
   )
   expect_equal(
-  length(attr(data, "Variables")$MPI_ESM),
-  3
-  )
-  expect_equal(
   length(attr(data, "Variables")$MPI_ESM$lon),
   30
   )
@@ -489,4 +934,43 @@ data <- Start(dataset = path_list,
   )
 
 
+suppressWarnings(
+dataF <- Start(dataset = path_list,
+              var = 'tasmin',
+              member = list(c('r1i1p1f1', 'r2i1p1f2')),
+              sdate = paste0(2018),
+              chunk = list(c('20181101-20281231', '20181101-20181230')),
+              time = indices(1), #'all',
+              lat = values(list(0, 14)),
+              lon = values(list(0, 28)),
+              synonims = list(time = c('fmonth','time'),
+                              lon = c('lon', 'longitude'),
+                              lat = c('lat', 'latitude')),
+              return_vars = list(lat = 'dataset', lon = 'dataset'),
+              lat_reorder = Sort(),
+              num_procs = 1,
+              retrieve = F)
+)
+
+  expect_equal(
+  length(attr(dataF, "Variables")$MPI_ESM$lon),
+  30
+  )
+  expect_equal(
+  names(attr(dataF, "Variables")$MPI_ESM),
+  c('lat', 'lon', 'tasmin')
+  )
+  expect_equal(
+  length(attr(dataF, "Variables")$MPI_ESM$tasmin),
+  22
+  )
+  expect_equal(
+  names(attr(dataF, "Variables")$HadGEM3),
+  c('lat', 'lon')
+  )
+  expect_equal(
+  length(attr(dataF, "Variables")$HadGEM3$lon),
+  34
+  )
+
 })
diff --git a/tests/testthat/test-Start-metadata_reshaping.R b/tests/testthat/test-Start-metadata_reshaping.R
index ac332cd..7e9c280 100644
--- a/tests/testthat/test-Start-metadata_reshaping.R
+++ b/tests/testthat/test-Start-metadata_reshaping.R
@@ -651,7 +651,7 @@ data <- Start(dat = paste0('/esarchive/recon/ecmwf/erainterim/6hourly/',
 )
 expect_equal(
 names(attributes(data)$Variables$common),
-NULL
+"tas"
 )
 
 })
-- 
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