Update code and tests to use hms instead of lubridate

DESCRIPTION

@@ -26,7 +26,7 @@ Depends: R (>= 4.0)
 Imports:
     yyjsonr (>= 0.1.18),
     jsonvalidate (>= 1.3.1),
-    lubridate
+    hms
 Suggests:
     testthat (>= 2.1.0),
     jsonlite (>= 1.8.0),

NAMESPACE

@@ -16,8 +16,8 @@ export(set_study_oid)
 export(set_variable_attributes)
 export(validate_dataset_json)
 export(write_dataset_json)
+importFrom(hms,as_hms)
 importFrom(jsonvalidate,json_validate)
-importFrom(lubridate,hms)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,tail)
 importFrom(yyjsonr,opts_read_json)

R/utils.R

@@ -127,7 +127,7 @@ date_time_conversions <- function(d, dt, tdt){
                              as.POSIXct,
                              tz = "UTC",
                              tryFormats = "%Y-%m-%dT%H:%M:%S")
-  d[time_cols] <- lapply(d[time_cols], hms)
+  d[time_cols] <- lapply(d[time_cols], as_hms)
   d
 }
 

R/zzz.R

@@ -2,7 +2,7 @@
 #' @importFrom yyjsonr opts_write_json opts_read_json write_json_file write_json_str read_json_str read_json_file
 #' @importFrom tools file_path_sans_ext
 #' @importFrom utils tail
-#' @importFrom lubridate hms
+#' @importFrom hms as_hms
 NULL
 
 #' @keywords internal

data-raw/data.R

@@ -89,7 +89,7 @@ time_options <- c("12:34:56", "15:34:34", "11:12:52", "21:16:11")
 
 adsl$VIST1TMC <- sample(time_options, 254, replace=TRUE)
 adsl$VIST1DTC <-paste(format(adsl$VISIT1DT, "%Y-%m-%d"), sample(time_options, 254, replace=TRUE), sep="T")
-adsl$VISIT1TM <- lubridate::hms(adsl$VIST1TMC)
+adsl$VISIT1TM <- hms::as_hms(adsl$VIST1TMC)
 adsl$VIST1DTM <- as.POSIXct(strptime(adsl$VIST1DTC, "%Y-%m-%dT%H:%M:%S", tz="UTC"))
 
 new_meta <- tibble::tribble(

tests/testthat/test-read_dataset_json.R

@@ -84,11 +84,11 @@ test_that("datetime conversions work properly",{
   iris_timetest <- read_dataset_json(test_path("testdata", "iris_timetest.json"))
 
   expect_s3_class(iris_timetest$Datetime, "POSIXct")
-  expect_equal(class(iris_timetest$Time), "Period", ignore_attr=TRUE)
+  expect_equal(class(iris_timetest$Time), c("hms", "difftime"), ignore_attr=TRUE)
 
   expect_equal(sort(unique(iris_timetest$Datetime)),
                as.POSIXct(strptime(c("2024-01-01T12:34:56", "2024-01-17T18:45:56"),
                         "%Y-%m-%dT%H:%M:%S", tz="UTC")))
   expect_equal(sort(unique(as.numeric(iris_timetest$Time))),
-               as.numeric(hms(c("12:34:56", "18:45:56"))))
+               as.numeric(as_hms(c("12:34:56", "18:45:56"))))
 })

tests/testthat/test-utils.R

@@ -42,5 +42,5 @@ test_that("Date, datetime and time conversions work as expected", {
   expect_equal(df_converted$datetime, as.POSIXct(c("2020-01-01 12:00:00",
                                                    "2020-01-01 12:00:01",
                                                    NA), tz = "UTC"))
-  expect_equal(df_converted$time, hms(c("12:00:00", "12:00:01", NA)))
+  expect_equal(df_converted$time, as_hms(c("12:00:00", "12:00:01", NA)))
 })

vignettes/converting_files.Rmd

@@ -49,6 +49,9 @@ extract_xpt_meta <- function(n, .data) {
   } else if (inherits(.data[[n]],"numeric")) {
     if (any(is.double(.data[[n]]))) out$dataType <- "float"
     else out$dataType <- "integer"
+  }  else if (inherits(.data[[n]],"hms")) {
+    out$dataType <- "time"
+    out$targetDataType <- "integer"
   } else {
     out$dataType <- "string"
     out$length <- max(purrr::map_int(.data[[n]], nchar))