Modify time unit judgement to consider the time variable that doesn't have name 'time'.

R/NcDataReader.R

@@ -184,8 +184,17 @@ NcDataReader <- function(file_path = NULL, file_object = NULL,
       })
 
     if (length(names(attr(result, 'variables'))) == 1) {
-      # The 1st condition is for implicit time dim (if time length = 1, it is allowed to not be defined in Start call. Therefore, it is not in the list of synonims)
-      if (names(attr(result, 'variables')) == 'time' | 'time' %in% synonims[[names(attr(result, 'variables'))]]) {
+      # The 1st condition is for implicit time dim (if time length = 1, it is 
+      # allowed to not be defined in Start call. Therefore, it is not in the list
+      # of synonims);
+      # the 2nd condition is for the normal case; the 3rd one is that if return_vars
+      # has a variable that is not 'time'. The only way to know if it should be time
+      # is to check calendar.
+      # All these conditions are to prevent the variables with time-like units but 
+      # actually not a time variable, e.g., drought period [days].
+      if (names(attr(result, 'variables')) == 'time' |
+          'time' %in% synonims[[names(attr(result, 'variables'))]] |
+          'calendar' %in% names(attr(result, 'variables')[[1]])) {
         var_name <- names(attr(result, 'variables'))
         units <- attr(result, 'variables')[[var_name]][['units']]
 

R/zzz.R

@@ -1430,7 +1430,7 @@ generate_picked_var_of_read <- function(var_to_read, var_to_check, array_of_file
     if (any(names(array_var_dims) %in% names(var_file_dims))) {
       array_var_dims <- array_var_dims[-which(names(array_var_dims) %in% names(var_file_dims))]
     }
-    if (names(array_var_dims) != names(var_dims)) {
+    if (any(names(array_var_dims) != names(var_dims))) {
       stop("Error while reading the variable '", var_to_read, "' from ",
            "the file. Dimensions do not match.\nExpected ",
            paste(paste0("'", names(array_var_dims), "'"), collapse = ', '),

tests/testthat/test-Start-implicit_inner_dim.R

@@ -3,6 +3,7 @@ context("Start() implicit inner dimension")
 # startR allows it not to be specified in the call. Users can still define it in 
 # 'return_vars'.
 #---------------------------------------------------------------
+#NOTE: Also useful for test-Start-time_unit.R test3
 
 test_that("1. time = 1", {
 

tests/testthat/test-Start-time_unit.R

+context("To detect the variable with time format and adjust the units")
+
+test_that("1. The data has units like time", {
+
+
+suppressWarnings(
+FD <- Start(dat = '/esarchive/obs/ukmo/hadex3/original_files/1961-90/HadEX3_$var$_MON.nc',
+            var = 'FD',  # units: days
+            time = indices(1),
+            longitude = indices(1), 
+            latitude = indices(1),
+            num_procs = 1, 
+            return_vars = list(time = NULL),
+            retrieve = TRUE)
+)
+suppressWarnings(
+FD2 <- Start(dat = '/esarchive/obs/ukmo/hadex3/original_files/1961-90/HadEX3_$var$_MON.nc',
+            var = 'FD',  # units: days
+            time = indices(1),
+            longitude = indices(1),
+            latitude = indices(1),
+            num_procs = 1,
+#            return_vars = list(time = NULL),
+            retrieve = TRUE)
+)
+expect_equal(
+attr(FD, 'Variables')$common$FD$units,
+'days'
+)
+expect_equal(
+attr(FD2, 'Variables')$common$FD$units,
+'days'
+)
+
+
+})
+
+test_that("2. The metadata variable name is not time", {
+# VITIGEOOS
+
+vari <- "rsds"
+anlgs <- paste0("/esarchive/oper/VITIGEOSS","/output/cfsv2/weekly_mean/",
+                "$var$/$var$-vitigeoss-cat","_1999-2018_", "$file_date$.nc")
+
+file_date_array <- array(dim = c(sweek = 2, sday = 3))
+file_date_array[, 1] <- c(paste0('04', c('04', '07')))
+file_date_array[, 2] <- c(paste0('04', c('07', '11')))
+file_date_array[, 3] <- c(paste0('04', c('11', '14')))
+
+suppressWarnings(
+  hcst <- Start(dat = anlgs,
+                var = vari,
+                latitude = indices(1), #'all', 
+                longitude= indices(1), #'all', 
+                member= indices(1), #'all', 
+                time = 'all',  # inner dim!!
+                syear = 'all', #inner dim!!
+                file_date = file_date_array,
+                split_multiselected_dims = TRUE,
+                retrieve = T,
+                return_vars = list(leadtimes = 'file_date'),
+                synonims = list(longitude = c('lon', 'longitude'),
+                                latitude = c('lat', 'latitude'),
+                                syear = c('sdate','syear'),
+                                member = c('ensemble','member')))
+)
+time_attr <- attr(hcst, 'Variables')$common$leadtimes
+
+expect_equal(
+dim(time_attr),
+c(sweek = 2, sday = 3, syear = 20, time = 4)
+)
+expect_equal(
+time_attr[,1,1,1],
+as.POSIXct(c("1999-04-08","1999-04-11"), tz = "UTC")
+)
+expect_equal(
+time_attr[2,,1,1],
+as.POSIXct(c("1999-04-11","1999-04-15", "1999-04-18"), tz = "UTC")
+)
+expect_equal(
+time_attr[1,1,20,],
+as.POSIXct(c("2018-04-08", "2018-04-15", "2018-04-22 UTC", "2018-04-29 UTC"), tz = "UTC")
+)
+
+})
+
+
+#test_that("3. Time dimension is implicit", {
+# See test-Start-implicit_inner_dim.R
+#})