[r] Support for dense current domain with core 2.27 (#3180)

* [r] Support for dense current domain with core 2.27

* fix unit-test cases

apis/r/R/Init.R

@@ -34,6 +34,11 @@
     .pkgenv[["use_current_domain_transitional_internal_only"]]
 }
 
+.dense_arrays_can_have_current_domain <- function() {
+  triple <- tiledb_embedded_version()
+  return(triple[[1]] >= 2 && triple[[2]] >= 27)
+}
+
 ## An .onAttach() function is not allowed to use cat() etc but _must_ communicate via
 ## packageStartupMessage() as this function can be 'muzzled' as desired. See Writing R Extensions.
 .onAttach <- function(libname, pkgname) {

apis/r/R/SOMANDArrayBase.R

@@ -90,6 +90,42 @@ SOMANDArrayBase <- R6::R6Class(
     #' @return Logical
     tiledbsoma_has_upgraded_shape = function() {
       has_current_domain(self$uri, private$.soma_context)
+    },
+
+    #' @description Increases the shape of the array as specfied. Raises an error
+    #' if the new shape is less than the current shape in any dimension. Raises
+    #' an error if the new shape exceeds maxshape in any dimension. Raises an
+    #' error if the array doesn't already have a shape: in that case please call
+    #' tiledbsoma_upgrade_shape.
+    #' @param new_shape A vector of integerish, of the same length as the array's `ndim`.
+    #' @return No return value
+    resize = function(new_shape) {
+      stopifnot(
+        "resize is not supported for dense arrays until tiledbsoma 1.15" =
+          .dense_arrays_can_have_current_domain() || private$.is_sparse,
+        "'new_shape' must be a vector of integerish values, of the same length as maxshape" =
+        rlang::is_integerish(new_shape, n = self$ndim()) ||
+          (bit64::is.integer64(new_shape) && length(new_shape) == self$ndim())
+      )
+      # Checking slotwise new shape >= old shape, and <= max_shape, is already done in libtiledbsoma
+      resize(self$uri, new_shape, private$.soma_context)
+    },
+
+    #' @description Allows the array to have a resizeable shape as described in the
+    #' TileDB-SOMA 1.15 release notes.  Raises an error if the shape exceeds maxshape in any
+    #' dimension. Raises an error if the array already has a shape.
+    #' @param shape A vector of integerish, of the same length as the array's `ndim`.
+    #' @return No return value
+    tiledbsoma_upgrade_shape = function(shape) {
+      stopifnot(
+        "tiledbsoma_upgrade_shape is not supported for dense arrays until tiledbsoma 1.15" =
+          .dense_arrays_can_have_current_domain() || private$.is_sparse,
+        "'shape' must be a vector of integerish values, of the same length as maxshape" =
+        rlang::is_integerish(shape, n = self$ndim()) ||
+          (bit64::is.integer64(shape) && length(shape) == self$ndim())
+      )
+      # Checking slotwise new shape >= old shape, and <= max_shape, is already done in libtiledbsoma
+      tiledbsoma_upgrade_shape(self$uri, shape, private$.soma_context)
     }
 
   ),

apis/r/R/SOMASparseNDArray.R

@@ -190,40 +190,6 @@ SOMASparseNDArray <- R6::R6Class(
     #' @return A scalar with the number of non-zero elements
     nnz = function() {
       nnz(self$uri, private$.soma_context)
-    },
-
-    #' @description Increases the shape of the array as specfied. Raises an error
-    #' if the new shape is less than the current shape in any dimension. Raises
-    #' an error if the new shape exceeds maxshape in any dimension. Raises an
-    #' error if the array doesn't already have a shape: in that case please call
-    #' tiledbsoma_upgrade_shape.
-    #' @param new_shape A vector of integerish, of the same length as the array's `ndim`.
-    #' @return No return value
-    resize = function(new_shape) {
-      # TODO: move this to SOMANDArrayBase.R once core offers current-domain support for dense arrays.
-      # https://github.com/single-cell-data/TileDB-SOMA/issues/2955
-
-      stopifnot("'new_shape' must be a vector of integerish values, of the same length as maxshape" = rlang::is_integerish(new_shape, n = self$ndim()) ||
-        (bit64::is.integer64(new_shape) && length(new_shape) == self$ndim())
-      )
-      # Checking slotwise new shape >= old shape, and <= max_shape, is already done in libtiledbsoma
-      resize(self$uri, new_shape, private$.soma_context)
-    },
-
-    #' @description Allows the array to have a resizeable shape as described in the
-    #' TileDB-SOMA 1.15 release notes.  Raises an error if the shape exceeds maxshape in any
-    #' dimension. Raises an error if the array already has a shape.
-    #' @param shape A vector of integerish, of the same length as the array's `ndim`.
-    #' @return No return value
-    tiledbsoma_upgrade_shape = function(shape) {
-      # TODO: move this to SOMANDArrayBase.R once core offers current-domain support for dense arrays.
-      # https://github.com/single-cell-data/TileDB-SOMA/issues/2955
-
-      stopifnot("'shape' must be a vector of integerish values, of the same length as maxshape" = rlang::is_integerish(shape, n = self$ndim()) ||
-        (bit64::is.integer64(shape) && length(shape) == self$ndim())
-      )
-      # Checking slotwise new shape >= old shape, and <= max_shape, is already done in libtiledbsoma
-      tiledbsoma_upgrade_shape(self$uri, shape, private$.soma_context)
     }
 
   ),

apis/r/R/utils-arrow.R

@@ -571,10 +571,7 @@ get_domain_and_extent_array <- function(shape, is_sparse) {
         # expansion.
         ind_max_dom <- arrow_type_unsigned_range(ind_col_type) - c(0,ind_ext)
 
-        # TODO: support current domain for dense arrays once we have that support
-        # from core.
-        # https://github.com/single-cell-data/TileDB-SOMA/issues/2955
-        if (.new_shape_feature_flag_is_enabled() && is_sparse) {
+        if (.new_shape_feature_flag_is_enabled() && (is_sparse || .dense_arrays_can_have_current_domain())) {
             aa <- arrow::arrow_array(c(ind_max_dom, ind_ext, ind_cur_dom), ind_col_type)
         } else {
             aa <- arrow::arrow_array(c(ind_cur_dom, ind_ext), ind_col_type)

apis/r/tests/testthat/test-shape.R

@@ -435,7 +435,8 @@ test_that("SOMASparseNDArray shape", {
 
       # Test resize up
       new_shape <- c(500, 600)
-      expect_no_error(ndarray$resize(new_shape))
+      ####expect_no_error(ndarray$resize(new_shape))
+      ndarray$resize(new_shape)
 
       # Test writes within new bounds
       soma_dim_0 <- c(200,300)
@@ -478,13 +479,17 @@ test_that("SOMADenseNDArray shape", {
     readback_shape <- ndarray$shape()
     readback_maxshape <- ndarray$maxshape()
     expect_equal(length(readback_shape), length(readback_maxshape))
-    # TODO: Awaiting core support for new shape in dense arrays.
-    # https://github.com/single-cell-data/TileDB-SOMA/issues/2955
-    #if (.new_shape_feature_flag_is_enabled()) {
-    #  expect_true(all(readback_shape < readback_maxshape))
-    #} else {
-    #  expect_true(all(readback_shape == readback_maxshape))
-    #}
+
+    if (.new_shape_feature_flag_is_enabled()) {
+      if (.dense_arrays_can_have_current_domain()) {
+        expect_true(all(readback_shape < readback_maxshape))
+      } else {
+        expect_true(all(readback_shape == readback_maxshape))
+      }
+    } else {
+      expect_true(all(readback_shape == readback_maxshape))
+    }
+
     expect_true(all(readback_shape == readback_maxshape))
 
     ndarray$close()
@@ -523,26 +528,29 @@ test_that("SOMADenseNDArray shape", {
 
       # Test resize up
       new_shape <- c(500, 600)
-      # TODO: Awaiting core support for new shape in dense arrays.
-      # https://github.com/single-cell-data/TileDB-SOMA/issues/2955
-      # expect_no_error(ndarray$resize(new_shape))
-      expect_error(ndarray$resize(new_shape))
+      if (tiledbsoma:::.dense_arrays_can_have_current_domain()) {
+        expect_no_error(ndarray$resize(new_shape))
+      } else {
+        expect_error(ndarray$resize(new_shape))
+      }
 
       # Test writes within new bounds
       ndarray <- SOMADenseNDArrayOpen(uri, "WRITE")
       mat <- create_dense_matrix_with_int_dims(300, 400)
-      # TODO: Awaiting core support for new shape in dense arrays.
-      # https://github.com/single-cell-data/TileDB-SOMA/issues/2955
-      # expect_no_error(ndarray$write(sm))
-      expect_error(ndarray$write(sm))
+      if (tiledbsoma:::.dense_arrays_can_have_current_domain()) {
+        expect_no_error(ndarray$write(sm))
+      } else {
+        expect_error(ndarray$write(sm))
+      }
       ndarray$close()
 
       ndarray <- SOMADenseNDArrayOpen(uri)
       coords <- list(bit64::as.integer64(c(101,202)), bit64::as.integer64(c(3,4)))
-      # TODO: Awaiting core support for new shape in dense arrays.
-      # https://github.com/single-cell-data/TileDB-SOMA/issues/2955
-      # expect_no_error(x <- ndarray$read(coords=coords)$tables()$concat())
-      expect_error(x <- ndarray$read(coords=coords)$tables()$concat())
+      if (tiledbsoma:::.dense_arrays_can_have_current_domain()) {
+        expect_no_condition(x <- ndarray$read(coords=coords)$tables()$concat())
+      } else {
+        expect_error(x <- ndarray$read(coords=coords)$tables()$concat())
+      }
       ndarray$close()
     }