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Update to recent TileDB Embedded changes (#300)
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* update tests, and default to sparse in fromDataFrame

* also update help page

* add explicit 'dense dataframe' test

* protect new test against factor column for older R
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@eddelbuettel
eddelbuettel committed Sep 20, 2021
1 parent 0469664 commit 6439c50
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Showing 7 changed files with 33 additions and 18 deletions.
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) {

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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
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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")
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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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