should fix #33

AustralianAntarcticDivision · Nov 12, 2024 · 65f625d · 65f625d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: raadfiles
 Title: File Database Management for 'raadtools'
-Version: 0.1.4.9011
+Version: 0.1.4.9012
 Authors@R: c(person("Michael D.","Sumner", role = c("aut", "cre"), email = "michael.sumner@aad.gov.au"),
              person("Ben", "Raymond", role = "ctb"),
              person("Kimberlee", "Baldry", role = c("ctb"), comment = c(ORCID = "0000-0003-3286-8624")))
@@ -9,7 +9,7 @@ Depends:
     R (>= 3.3.0)
 Imports:
     digest,
-    fs (>= 1.6.4.9000),
+    fs (>= 1.6.5),
     rlang,
     stringr,
     dplyr,

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,7 @@
 # raadfiles dev
 
+* Fix problematic old UTC flush (thanks Dale Maschette #33). 
+
 * Avoid oldformat in Copernicus altimetry files. 
 
 

diff --git a/R/altimetry-antarctica.R b/R/altimetry-antarctica.R
@@ -113,7 +113,6 @@ pattern <- c("ftp-access.aviso.altimetry.fr",
   files <- dplyr::mutate(files, date = as.POSIXct(as.Date(stringr::str_extract(basename(.data$fullname), "[0-9]{8}"),
                                                           "%Y%m%d"),tz = "UTC"))
   dplyr::arrange(dplyr::distinct(files, date, .keep_all = TRUE), date)  %>%
-    dplyr::select(.data$date, .data$fullname, .data$root) %>%
-    set_dt_utc()
+    dplyr::select(.data$date, .data$fullname, .data$root)
 
 }
diff --git a/R/amps-files.R b/R/amps-files.R
@@ -46,10 +46,8 @@ amps_model_files <- function(time.resolution = "4hourly", grid = "d1", ...) {
                                              sprintf("_%s_", grid)))
   dplyr::transmute(files, hour = substr(basename(.data$fullname), 20, 22),
                    model = substr(basename(.data$fullname), 9, 10),
-                   date = as.POSIXct(strptime(basename(files$fullname), "%Y%m%d%H"), tz = "GMT") +
-                     as.integer(.data$hour) * 3600, .data$fullname, .data$root) %>%
-    set_dt_utc()
-
+                   date = as.POSIXct(strptime(basename(files$fullname), "%Y%m%d%H"), tz = "UTC") +
+                     as.integer(.data$hour) * 3600, .data$fullname, .data$root)
 
 }
 

diff --git a/R/cafe-modis.R b/R/cafe-modis.R
@@ -20,7 +20,6 @@ cafe_monthly_files <- function() {
   files <- dplyr::mutate(files, date = as.POSIXct(as.Date(stringr::str_extract(basename(.data$fullname), "[0-9]{7}"),
                                                           "%Y%j"),tz = "UTC"))
   dplyr::arrange(dplyr::distinct(files, date, .keep_all = TRUE), date)  %>%
-    dplyr::select(.data$date, .data$fullname, .data$root) %>%
-    set_dt_utc()
+    dplyr::select(.data$date, .data$fullname, .data$root)
 
 }
diff --git a/R/ccmpwind-files.R b/R/ccmpwind-files.R
@@ -38,8 +38,7 @@ ccmp_6hourly_files <- function() {
   ## put all NRT last before distinct by date
   files <- files[nrow(files):1, ]
 files <- dplyr::arrange(dplyr::distinct(files, .data$date, .keep_all = TRUE), date)  %>%
-    dplyr::select(.data$date, .data$fullname, .data$root) %>%
-    raadfiles:::set_dt_utc()
+    dplyr::select(.data$date, .data$fullname, .data$root)
 
   files
 }
diff --git a/R/fsle-files.R b/R/fsle-files.R
@@ -14,9 +14,8 @@ fsle_files <- function() {
     stop("no files found")
   ## datadir <- get_raad_datadir()
   files <- dplyr::mutate(files, date = as.POSIXct(as.Date(stringr::str_extract(basename(.data$fullname), "[0-9]{8}"),
-                                                          "%Y%m%d"),tz = "GMT"))
+                                                          "%Y%m%d"),tz = "UTC"))
   dplyr::arrange(dplyr::distinct(files, date, .keep_all = TRUE), date)  %>%
-    dplyr::select(.data$date, .data$fullname, .data$root) %>%
-    set_dt_utc()
+    dplyr::select(.data$date, .data$fullname, .data$root)
 }
 
diff --git a/R/ncep2-files.R b/R/ncep2-files.R
@@ -24,8 +24,7 @@ ncep2_uwnd_6hr_files <- function() {
     stop("no files found")
   files <- dplyr::transmute(files, date = ISOdate(as.integer(stringr::str_extract(basename(fullname), "[0-9]{4}")), 1, 1, 0, 0, 0, tz = "UTC"),
                          fullname = .data$fullname, root = .data$root)
-  dplyr::arrange(dplyr::distinct(files, .data$date, .keep_all = TRUE), .data$date) %>%
-    set_dt_utc()
+  dplyr::arrange(dplyr::distinct(files, .data$date, .keep_all = TRUE), .data$date)
 
 }
 #' @name ncep2_files
@@ -36,10 +35,9 @@ ncep2_vwnd_6hr_files <- function() {
 
   if (nrow(files) < 1)
     stop("no files found")
-  files <- dplyr::transmute(files, date = ISOdate(as.integer(stringr::str_extract(basename(fullname), "[0-9]{4}")), 1, 1),
+  files <- dplyr::transmute(files, date = ISOdate(as.integer(stringr::str_extract(basename(fullname), "[0-9]{4}")), 1, 1, tz  = "UTC"),
                          fullname = .data$fullname, root = .data$root)
-  dplyr::arrange(dplyr::distinct(files, .data$date, .keep_all = TRUE), .data$date) %>%
-    set_dt_utc()
+  dplyr::arrange(dplyr::distinct(files, .data$date, .keep_all = TRUE), .data$date)
 
 
 }

diff --git a/R/par-files.R b/R/par-files.R
@@ -25,7 +25,7 @@ if (nrow(files) < 1)
   files <- files[nrow(files):1, ]
   files <- dplyr::arrange(dplyr::distinct(files, .data$date,
                                           .keep_all = TRUE), date) %>% dplyr::select(.data$date,
-                                                                                     .data$fullname, .data$root) %>% raadfiles:::set_dt_utc()
+                                                                                     .data$fullname, .data$root)
 
   files
 }
diff --git a/R/seapodym-files.R b/R/seapodym-files.R
@@ -72,9 +72,8 @@ seapodym_weekly_files <- function() {
 
   ## datadir <- get_raad_datadir()
   files <- dplyr::mutate(files, date = as.POSIXct(as.Date(stringr::str_extract(basename(.data$fullname), "[0-9]{8}"),
-                                                          "%Y%m%d"),tz = "GMT"))
+                                                          "%Y%m%d"),tz = "UTC"))
   dplyr::arrange(dplyr::distinct(files, date, .keep_all = TRUE), date)  %>%
-    dplyr::select(.data$date, .data$fullname, .data$root) %>%
-    set_dt_utc()
+    dplyr::select(.data$date, .data$fullname, .data$root)
 
 }
diff --git a/R/smap-files.R b/R/smap-files.R
@@ -28,7 +28,6 @@ smap_8day_files <- function() {
 
 files$date <- as.POSIXct(strptime(sprintf("%s-%s", Y, jday), "%Y-%j"), tz = "UTC") #as.POSIXct(strptime(basename(.data$fullname), "RSS_smap_SSS_L3_8day_running_40km"), tz = "UTC"))
   files <- dplyr::arrange(dplyr::distinct(files, date, .keep_all = TRUE), date)  %>%
-    dplyr::select(.data$date, .data$fullname, .data$root) %>%
-    raadfiles:::set_dt_utc()
+    dplyr::select(.data$date, .data$fullname, .data$root)
   files
 }
diff --git a/R/sst-files.R b/R/sst-files.R
@@ -33,10 +33,10 @@ oisst_daily_files <- function() {
     stop("no files found")
   }
   files <- dplyr::mutate(files, date = as.POSIXct(as.Date(stringr::str_extract(basename(.data$fullname), "[0-9]{8}"),
-                                                          "%Y%m%d"),tz = "GMT"))
+                                                          "%Y%m%d"),tz = "UTC"))
   dplyr::arrange(dplyr::distinct(files, date, .keep_all = TRUE), date)  %>%
-    dplyr::select(.data$date, .data$fullname, .data$root) %>%
-    set_dt_utc()
+    dplyr::select(.data$date, .data$fullname, .data$root)
+
 }
 #' @name oisst
 #' @export

diff --git a/R/utils.R b/R/utils.R
@@ -26,35 +26,6 @@ globalVariables("desc")  ## for dplyr in arrange()
 }
 
 
-
-set_utc_md <- function(x) {
-  attr(x, "tzone") <- "UTC"
-  x
-}
-## apply UTC metadata for print (raadtools#72)
-set_dt_utc <- function(x) {
-  x[["date"]] <- set_utc_md(x[["date"]])
-
-  ## and do sanity checks on last 20 files
-  files <- x[["fullname"]]
-  if (is.null(files)) {
-    files <- x[["ufullname"]]
-    if (is.null(files)) files <- x[["vfullname"]]
-  }
-
-  if (!is.null(files)) {
-    sizes <- fs::file_size(tail(files, 20L))
-    bad <- !sizes > 0
-   if (any(bad)) {
-     message(sprintf("\n(please inform maintainers)\n\n problem with zero-size files near\n %s\n", files[which(bad)[1L]]))
-      idx <- c(rep(TRUE, dim(x)[1L] - 20), !bad)
-      x <- x[idx, ]
-   }
-  }
-  x
-}
-
-
 ## file cache utilities
 
 remove_leading_slash <- function(x) {