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Update to recent TileDB Embedded changes #300

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merged 4 commits into from Sep 20, 2021
Merged

Update to recent TileDB Embedded changes #300

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e03633a
update tests, and default to sparse in fromDataFrame
eddelbuettel Sep 20, 2021
064bcca
also update help page
eddelbuettel Sep 20, 2021
b9e80f3
add explicit 'dense dataframe' test
eddelbuettel Sep 20, 2021
c21781e
protect new test against factor column for older R
eddelbuettel Sep 20, 2021
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -27,5 +27,5 @@ LinkingTo: Rcpp
Suggests: tinytest, rmarkdown, knitr, minidown, curl, bit64, Matrix, palmerpenguins, nycflights13, data.table, tibble
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
RoxygenNote: 7.1.2
Encoding: UTF-8
4 changes: 2 additions & 2 deletions R/DataFrame.R
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Expand Up @@ -40,7 +40,7 @@
##' @param col_index An optional column index, either numeric with a column index,
##' or character with a column name, designating an index column; default is NULL
##' implying an index column is added when the array is created
##' @param sparse A logical switch to select sparse or dense (the default)
##' @param sparse A logical switch to select sparse (the default) or dense
##' @param allows_dups A logical switch to select if duplicate values
##' are allowed or not, default is the same value as \sQuote{sparse}.
##' @param cell_order A character variable with one of the TileDB cell order values,
Expand Down Expand Up @@ -71,7 +71,7 @@
##' all.equal(iris, newdf)
##' }
##' @export
fromDataFrame <- function(obj, uri, col_index=NULL, sparse=FALSE, allows_dups=sparse,
fromDataFrame <- function(obj, uri, col_index=NULL, sparse=TRUE, allows_dups=sparse,
cell_order = "COL_MAJOR", tile_order = "COL_MAJOR", filter="ZSTD",
capacity = 10000L, tile_domain = NULL, tile_extent = NULL, debug = FALSE) {

Expand Down
4 changes: 2 additions & 2 deletions inst/tinytest/test_arrowio.R
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Expand Up @@ -52,7 +52,7 @@ sch <- tiledb_array_schema(dom,
tiledb_attr("int64", type="INT64"),
tiledb_attr("uint64", type="UINT64"),
tiledb_attr("float64",type="FLOAT64")),
sparse = FALSE)
sparse = TRUE)
tiledb_array_create(tmp, sch)

arr <- tiledb_array(tmp)
Expand Down Expand Up @@ -126,7 +126,7 @@ sch <- tiledb_array_schema(dom,
tiledb_attr("int64", type="INT64"),
tiledb_attr("uint64", type="UINT64"),
tiledb_attr("float64",type="FLOAT64")),
sparse = FALSE)
sparse = TRUE)
tiledb_array_create(tmp, sch)

## create an arrow 'record batch' with a number of (correcsponding) columns
Expand Down
17 changes: 16 additions & 1 deletion inst/tinytest/test_dataframe.R
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Expand Up @@ -37,7 +37,7 @@ expect_equivalent(iris[, c("Petal.Length", "Petal.Width")], newdf) # skip attrib


## test list
arr <- tiledb_array(uri)
arr <- tiledb_array(uri, return_as="asis")
res <- arr[]
expect_equal(class(res), "list")
expect_equal(length(res), 6) # plus one for 'rows'
Expand Down Expand Up @@ -266,3 +266,18 @@ arr <- tiledb_array(uri, as.data.frame=TRUE)
chk <- arr[]
if (getRversion() < '4.0.0') chk$char <- as.character(chk$char)
expect_equivalent(df, chk) # skip attribute

## explicit dense data.frame
df <- data.frame(aa=1:26,
bb=26:1,
cc=letters,
dd=LETTERS)
uri <- tempfile()
fromDataFrame(df, uri, sparse=FALSE)
arr <- tiledb_array(uri, return_as="data.frame", extended=FALSE) # skip row index on return
res <- arr[]
if (getRversion() < '4.0.0') {
res$cc <- as.character(res$cc)
res$dd <- as.character(res$dd)
}
expect_equivalent(df, res)
2 changes: 1 addition & 1 deletion inst/tinytest/test_query.R
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Expand Up @@ -158,7 +158,7 @@ dom <- tiledb_domain(dims = tiledb_dim("rows", c(1L, 10L), 1L, type = "INT32"))
schema <- tiledb_array_schema(dom,
attrs = c(tiledb_attr("vals", type = "INT32"),
tiledb_attr("keys", type = "INT32", nullable = TRUE)),
sparse=FALSE)
sparse=TRUE)
tiledb_array_create(tmp, schema)
arr <- tiledb_array(tmp)
qry <- tiledb_query(arr, "WRITE")
Expand Down
18 changes: 9 additions & 9 deletions inst/tinytest/test_tiledbarray.R
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Expand Up @@ -586,7 +586,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
## The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4]
dom <- tiledb_domain(dims = c(tiledb_dim("rows", c(1L,4L), 4L, "INT8"),
tiledb_dim("cols", c(1L,4L), 4L, "INT8")))
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=FALSE)
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down Expand Up @@ -617,7 +617,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
## The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4]
dom <- tiledb_domain(dims = c(tiledb_dim("rows", c(1L,4L), 4L, "UINT8"),
tiledb_dim("cols", c(1L,4L), 4L, "UINT8")))
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=FALSE)
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down Expand Up @@ -648,7 +648,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
## The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4]
dom <- tiledb_domain(dims = c(tiledb_dim("rows", c(1L,4L), 4L, "INT16"),
tiledb_dim("cols", c(1L,4L), 4L, "INT16")))
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=FALSE)
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down Expand Up @@ -679,7 +679,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
## The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4]
dom <- tiledb_domain(dims = c(tiledb_dim("rows", c(1L,4L), 4L, "UINT16"),
tiledb_dim("cols", c(1L,4L), 4L, "UINT16")))
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=FALSE)
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down Expand Up @@ -710,7 +710,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
## The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4]
dom <- tiledb_domain(dims = c(tiledb_dim("rows", c(1L,4L), 4L, "INT32"),
tiledb_dim("cols", c(1L,4L), 4L, "INT32")))
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=FALSE)
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down Expand Up @@ -741,7 +741,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
## The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4]
dom <- tiledb_domain(dims = c(tiledb_dim("rows", c(1L,4L), 4L, "UINT32"),
tiledb_dim("cols", c(1L,4L), 4L, "UINT32")))
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=FALSE)
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down Expand Up @@ -772,7 +772,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
## The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4]
dom <- tiledb_domain(dims = c(tiledb_dim("rows", as.integer64(c(1,4)), as.integer64(4), "INT64"),
tiledb_dim("cols", as.integer64(c(1,4)), as.integer64(4), "INT64")))
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=FALSE)
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down Expand Up @@ -804,7 +804,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
## The array will be 4x4 with dimensions "rows" and "cols", with domain [1,4]
dom <- tiledb_domain(dims = c(tiledb_dim("rows", as.integer64(c(1,4)), as.integer64(4), "UINT64"),
tiledb_dim("cols", as.integer64(c(1,4)), as.integer64(4), "UINT64")))
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=FALSE)
schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")), sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down Expand Up @@ -846,7 +846,7 @@ if (requireNamespace("bit64", quietly=TRUE)) {
tiledb_attr("a7", type = "INT64"),
tiledb_attr("a8", type = "UINT64")
),
sparse=FALSE)
sparse=TRUE)
tiledb_array_create(uri = tmp, schema)
#print(schema)
A <- tiledb_array(uri = tmp)
Expand Down
4 changes: 2 additions & 2 deletions man/fromDataFrame.Rd
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