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Add support for character arrays in TileDBArray #28

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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: TileDBArray
Version: 1.15.4
Date: 2024-10-01
Version: 1.15.5
Date: 2025-04-24
Title: Using TileDB as a DelayedArray Backend
Description: Implements a DelayedArray backend for reading and
writing dense or sparse arrays in the TileDB format. The
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2 changes: 1 addition & 1 deletion R/TileDBArray.R
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Expand Up @@ -206,7 +206,7 @@ setMethod("path", "TileDBArraySeed", function(object, ...) {

#' @export
setMethod("extract_array", "TileDBArraySeed", function(x, index) {
fill <- switch(type(x), double=0, integer=0L, logical=FALSE)
fill <- switch(type(x), character="", double=0, integer=0L, logical=FALSE)
d2 <- .get_block_dims(x, index)

# Hack to overcome zero-length indices that cause tiledb to throw.
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4 changes: 3 additions & 1 deletion R/TileDBRealizationSink.R
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Expand Up @@ -151,11 +151,13 @@ TileDBRealizationSink <- function(
storagetype <- r_to_tiledb_type(vector(type))
}

ncells <- if (storagetype %in% c("ASCII", "CHAR", "UTF8")) NA_integer_ else 1L

schema <- tiledb_array_schema(
ctx=context,
domain=dom,
sparse=sparse,
attrs=list(tiledb_attr(ctx=context, attr, type=storagetype)),
attrs=list(tiledb_attr(attr, type=storagetype, ncells=ncells, ctx=context)),
cell_order = cellorder,
tile_order = tileorder,
capacity = capacity
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10 changes: 8 additions & 2 deletions tests/testthat/test-read.R
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Expand Up @@ -10,14 +10,17 @@ XD <- as(DD, "TileDBArray")
DL <- DD > 0
XL <- as(DL, "TileDBArray")

DC <- matrix(sample(letters, 10000, replace=TRUE), nrow=200)
XC <- as(DC, "TileDBArray")

SD <- Matrix::rsparsematrix(50, 50, density=0.1)
YD <- as(SD, "TileDBArray")

SL <- SD > 0
YL <- as(SL, "TileDBArray")

tdb <- list(XI, XD, XL, YD, YL)
ref <- list(DI, DD, DL, SD, SL)
tdb <- list(XI, XD, XL, XC, YD, YL)
ref <- list(DI, DD, DL, DC, SD, SL)

test_that("basic read operations work correctly ", {
for (x in seq_along(tdb)) {
Expand Down Expand Up @@ -63,6 +66,9 @@ test_that("more complex matrix operations work correctly", {
r <- ref[[x]]
t <- tdb[[x]]

if (is.character(r))
next

expect_equal(colSums(r), colSums(t))
expect_equal(rowSums(r), rowSums(t))

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3 changes: 2 additions & 1 deletion tests/testthat/test-write.R
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Expand Up @@ -4,11 +4,12 @@
DI <- matrix(rpois(10000, 5), nrow=200)
DD <- matrix(rnorm(10000), nrow=200)
DL <- DD > 0
DC <- matrix(sample(letters, 10000, replace=TRUE), nrow=200)

SD <- Matrix::rsparsematrix(50, 50, density=0.1)
SL <- SD > 0

ref <- list(DI, DD, DL, SD, SL)
ref <- list(DI, DD, DL, DC, SD, SL)

test_that("writing works as expected", {
for (x in seq_along(ref)) {
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