From 109452c8f9e569651ecc403f5e9d64bbe39f7b70 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Mon, 14 Sep 2020 15:48:04 +0200
Subject: [PATCH 1/3] Bugfix for metadata_dims along non-dat dim

---
 R/Start.R                                     |  18 +++--
 tests/testthat/.nfs00000000017f557800000031   | Bin 0 -> 16384 bytes
 .../testthat/test-Start-first_file_missing.R  |  69 ++++++++++++++++--
 3 files changed, 77 insertions(+), 10 deletions(-)
 create mode 100644 tests/testthat/.nfs00000000017f557800000031

diff --git a/R/Start.R b/R/Start.R
index 8243fda..be2e102 100644
--- a/R/Start.R
+++ b/R/Start.R
@@ -4218,19 +4218,27 @@ Start <- function(..., # dim = indices/selectors,
 
     } else {  #(1)
       var_backup <- attr(data_array, 'Variables')
-      var_backup_names <- unlist(lapply(var_backup, names))
-      new_list <- vector('list', length = length(var_backup_names))
+      len <- unlist(lapply(var_backup, length))
+      len <- sum(len) + length(which(len == 0))  #0 means NULL
+      name_list <- lapply(var_backup, names)
+      new_list <- vector('list', length = len)
       count <- 1
+
       for (kk in 1:length(var_backup)) {
-        for (jj in 1:length(var_backup[[kk]])) {
-          new_list[[count]] <- var_backup[[kk]][[jj]]
+        if (length(var_backup[[kk]]) == 0) {  #NULL
           count <- count + 1
+        } else {
+          for (jj in 1:length(var_backup[[kk]])) {
+            new_list[[count]] <- var_backup[[kk]][[jj]]
+            names(new_list)[count] <- name_list[[kk]][jj]
+            count <- count + 1
+          }
         }
       }
-      names(new_list) <- var_backup_names
       var_backup <- new_list
     }
 }
+
     attr(data_array, 'Variables') <- NULL
     attributes(data_array) <- c(attributes(data_array), 
                                 list(Variables = c(list(common = c(picked_common_vars, var_backup)), 
diff --git a/tests/testthat/.nfs00000000017f557800000031 b/tests/testthat/.nfs00000000017f557800000031
new file mode 100644
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diff --git a/tests/testthat/test-Start-first_file_missing.R b/tests/testthat/test-Start-first_file_missing.R
index 95319ae..25f4d02 100644
--- a/tests/testthat/test-Start-first_file_missing.R
+++ b/tests/testthat/test-Start-first_file_missing.R
@@ -12,7 +12,7 @@ sdates1 <- c('20130611')  #exists
 sdates2 <- c('20130618')  #does not exist
 sdates3 <- c("20130611", "20130618")  #1st exists, 2nd missing
 sdates4 <- c("20130618", "20130611")  #1st missing, 2nd exists
-
+sdates5 <- c("20130611", "20130612")  #both exist
 
 test_that("1. first file missing, no assign parameter 'metadata_dims'", {
 
@@ -69,7 +69,7 @@ data <- Start(dat = file,
               return_vars = list(latitude = 'dat',
                                  longitude = 'dat',
                                  time = 'file_date'),
-#              metadata_dims = c('file_date'),
+              metadata_dims = c('file_date'),
               retrieve = T)
 
   expect_equal(
@@ -87,11 +87,11 @@ data <- Start(dat = file,
   )
   expect_equal(
   names(attr(data, 'Variables')$common),
-  c('time')
+  c('time', NA, 'tas')
   )
 })
 
-test_that("3. Use parameter 'metadata_dims', all common attributes", {
+test_that("3. Use parameter 'metadata_dims', all common attributes, 1st file missing", {
 
 data <- Start(dat = file,
               var = var,
@@ -112,7 +112,7 @@ data <- Start(dat = file,
 
   expect_equal(
   names(attr(data, 'Variables')$common),
-  c('latitude', 'longitude', 'time', 'tas', NA)
+  c('latitude', 'longitude', 'time', NA, 'tas')
   )
   expect_equal(
   as.vector(attr(data, 'NotFoundFiles')),
@@ -121,3 +121,62 @@ data <- Start(dat = file,
 
 })
 
+test_that("4. Use parameter 'metadata_dims', all common attributes, 2nd file missing", {
+
+data <- Start(dat = file,
+              var = var,
+              file_date = sdates3,
+              time = indices(1:4),
+              latitude = values(list(20, 30)),
+              latitude_reorder = Sort(decreasing = TRUE),
+              longitude = values(list(-20, -10)),
+              longitude_reorder = CircularSort(-180, 180),
+              ensemble = indices(1),
+              synonims = list(latitude = c('lat', 'latitude'),
+                              longitude = c('lon', 'longitude')),
+              return_vars = list(latitude = NULL,
+                                 longitude = NULL,
+                                 time = 'file_date'),
+              metadata_dims = c('file_date'),
+              retrieve = T)
+
+  expect_equal(
+  names(attr(data, 'Variables')$common),
+  c('latitude', 'longitude', 'time', 'tas', NA)
+  )
+  expect_equal(
+  as.vector(attr(data, 'NotFoundFiles')),
+  c(NA, "/esarchive/exp/ncep/cfs-v2/weekly_mean/s2s/tas_f24h/tas_20130618.nc")
+  )
+
+})
+
+test_that("5. Use parameter 'metadata_dims', all common attributes, no file missing", {
+
+data <- Start(dat = file,
+              var = var,
+              file_date = sdates5,
+              time = indices(1:4),
+              latitude = values(list(20, 30)),
+              latitude_reorder = Sort(decreasing = TRUE),
+              longitude = values(list(-20, -10)),
+              longitude_reorder = CircularSort(-180, 180),
+              ensemble = indices(1),
+              synonims = list(latitude = c('lat', 'latitude'),
+                              longitude = c('lon', 'longitude')),
+              return_vars = list(latitude = NULL,
+                                 longitude = NULL,
+                                 time = 'file_date'),
+              metadata_dims = c('file_date'),
+              retrieve = T)
+
+  expect_equal(
+  names(attr(data, 'Variables')$common),
+  c('latitude', 'longitude', 'time', 'tas', 'tas')
+  )
+  expect_equal(
+  as.vector(attr(data, 'NotFoundFiles')),
+  NULL
+  )
+
+})
-- 
GitLab


From 60b9593ddbcb743e9c8682b29a558f1f4dbecfb5 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Mon, 14 Sep 2020 15:54:26 +0200
Subject: [PATCH 2/3] Remove trash file

---
 tests/testthat/.nfs00000000017f557800000031 | Bin 16384 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 tests/testthat/.nfs00000000017f557800000031

diff --git a/tests/testthat/.nfs00000000017f557800000031 b/tests/testthat/.nfs00000000017f557800000031
deleted file mode 100644
index c4163e5ad42853f122d402b905bc8dda4a954bbf..0000000000000000000000000000000000000000
GIT binary patch
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-- 
GitLab


From a4dfcb7fb477e32ef375810e7cde37e46d476dd3 Mon Sep 17 00:00:00 2001
From: aho <an.ho@bsc.es>
Date: Mon, 14 Sep 2020 16:31:53 +0200
Subject: [PATCH 3/3] Fix unit test attributes for R/3.6.1

---
 tests/testthat/test-Start-path_glob_permissive.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-Start-path_glob_permissive.R b/tests/testthat/test-Start-path_glob_permissive.R
index 9e14c02..fecb69d 100644
--- a/tests/testthat/test-Start-path_glob_permissive.R
+++ b/tests/testthat/test-Start-path_glob_permissive.R
@@ -38,7 +38,7 @@ data <- Start(dat = repos,
   )
   expect_equal(
   data[1, 1, , , 1, 1],
-  matrix(c(18.60422, 17.13862, 18.52348, 17.21780), 2, 2), 
+  array(c(18.60422, 17.13862, 18.52348, 17.21780), dim = c(expid = 2, year = 2)), 
   tolerance = 0.0001
   )
 
@@ -79,7 +79,7 @@ data <- Start(dat = repos,
   )
   expect_equal(
   data[1, 1, , , 1, 1, 1],
-  matrix(c(18.60422, 17.13862, 18.52348, 17.21780), 2, 2),
+  array(c(18.60422, 17.13862, 18.52348, 17.21780), dim = c(expid = 2, year = 2)),
   tolerance = 0.0001
   )
   expect_equal(
-- 
GitLab