Support explicit timestamps in fromDataFrame convenience helper (#719)

* Support explicit timestamps in fromDataFrame convenience helper

* Condition new tests on 2.15.0 or later

R/DataFrame.R

@@ -68,6 +68,10 @@
 ##' @param offsets_filters A character vector with filters for coordinates, default is \code{ZSTD}.
 ##' @param validity_filters A character vector with filters for coordinates, default is \code{RLE}.
 ##' @param debug Logical flag to select additional output.
+##' @param timestamps Vector with up to two \code{POSIXct} variables denoting open intervals; default
+##' is length zero where start and end are set (implicitly) to current time; in case of one value it
+##' is used as the interval end, and in case of two values they are taken as start and end. This
+##' applies to write and append modes only and not to schema creation.
 ##' @return Null, invisibly.
 ##' @examples
 ##' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
@@ -83,10 +87,13 @@ fromDataFrame <- function(obj, uri, col_index=NULL, sparse=TRUE, allows_dups=spa
                           capacity = 10000L, tile_domain = NULL, tile_extent = NULL,
                           mode = c("ingest", "schema_only", "append"), filter_list = NULL,
                           coords_filters = "ZSTD", offsets_filters = "ZSTD",
-                          validity_filters = "RLE", debug = FALSE) {
+                          validity_filters = "RLE", debug = FALSE,
+                          timestamps = as.POSIXct(double(), origin="1970-01-01")) {
 
     stopifnot("Argument 'obj' should be a 'data.frame' (or a related object)" = inherits(obj, "data.frame"),
-              "Argument 'uri' should be a character variable" = is.character(uri))
+              "Argument 'uri' should be a character variable" = is.character(uri),
+              "Argument 'timestamps' must be a POSIXct vector" = inherits(timestamps, "POSIXct"),
+              "Argument 'timestamps' must be 0, 1 or 2 values" = length(timestamps) %in% c(0L, 1L, 2L))
     if (!is.null(col_index) && is.character(col_index)) col_index <- match(col_index, colnames(obj))
     dims <- dim(obj)
     mode <- match.arg(mode)
@@ -276,7 +283,10 @@ fromDataFrame <- function(obj, uri, col_index=NULL, sparse=TRUE, allows_dups=spa
         tiledb_array_create(uri, schema)
 
     if (mode != "schema_only") {
-        df <- tiledb_array(uri, query_type = "WRITE")
+        df <- switch(length(timestamps) + 1, 		# switch takes ints starting at one
+                     tiledb_array(uri, query_type = "WRITE"),
+                     tiledb_array(uri, query_type = "WRITE", timestamp_end=timestamps[1]),
+                     tiledb_array(uri, query_type = "WRITE", timestamp_start=timestamps[1], timestamp_end=timestamps[2]))
         ## when setting an index when likely want 'sparse write to dense array
         if (!is.null(col_index) && !sparse)
             query_layout(df) <- "UNORDERED"

inst/tinytest/test_dataframe.R

@@ -340,3 +340,28 @@ fromDataFrame(D, uri, col_index=1)
 arr <- tiledb_array(uri, return_as="data.frame")
 res <- arr[]
 expect_equivalent(res, D)
+
+
+## fromDataFrame with timestamps
+if (tiledb_version(TRUE) < "2.15.0") exit_file("Remaining tests require TileDB 2.15.0 or later")
+D <- data.frame(key=(1:10)*10, value=letters[1:10])
+uri <- tempfile()
+now <- Sys.time()
+fromDataFrame(D, uri)         # no timestamps
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame")[]), 10)
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame", timestamp_end=as.POSIXct(100, origin="1970-01-01"))[]),  0)
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame", timestamp_start=now + 1)[]), 0)
+unlink(uri, recursive=TRUE)
+
+fromDataFrame(D, uri, timestamps=as.POSIXct(100, origin="1970-01-01"))         # end timestamps
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame")[]), 10)
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame", timestamp_end=as.POSIXct(50, origin="1970-01-01"))[]), 0)
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame", timestamp_start=as.POSIXct(50, origin="1970-01-01"))[]), 10)
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame", timestamp_start=as.POSIXct(150, origin="1970-01-01"))[]), 0)
+unlink(uri, recursive=TRUE)
+
+fromDataFrame(D, uri, timestamps=c(as.POSIXct(100, origin="1970-01-01"), as.POSIXct(100, origin="1970-01-01"))) # start and end
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame")[]), 10)
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame", timestamp_end=as.POSIXct(50, origin="1970-01-01"))[]), 0)
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame", timestamp_start=as.POSIXct(50, origin="1970-01-01"))[]), 10)
+expect_equal(nrow(tiledb_array(uri, return_as="data.frame", timestamp_start=as.POSIXct(150, origin="1970-01-01"))[]), 0)

inst/tinytest/test_timetravel.R

@@ -172,7 +172,7 @@ invisible( tiledb_array_create(tmp, schema) )
 I <- c(1, 2, 2)
 J <- c(1, 4, 3)
 data <- c(1L, 2L, 3L)
-now1 <- as.POSIXct(60, tz="UTC") 		# the epoch plus one minute
+now1 <- as.POSIXct(60, tz="UTC", origin="1970-01-01") 	# the epoch plus one minute
 A <- tiledb_array(uri = tmp, timestamp_start=now1, timestamp_end=now1)
 A[I, J] <- data