Update the dense example, add a memfs one

inst/examples/quickstart_dense.R

@@ -5,7 +5,7 @@
 #
 # The MIT License
 #
-# Copyright (c) 2018-2020 TileDB, Inc.
+# Copyright (c) 2018-2021 TileDB, Inc.
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -56,7 +56,7 @@ create_array <- function(uri) {
     schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")))
 
     # Create the (empty) array on disk.
-    tiledb_array_create(uri, schema)
+    invisible(tiledb_array_create(uri, schema))
 }
 
 write_array <- function(uri) {
@@ -85,11 +85,11 @@ write_array_via_query_piped <- function(uri) {
     stopifnot(requireNamespace("magrittr", quietly=TRUE))
     library(magrittr)
     data <- 1:16
-    qry <- tiledb_array(uri = uri) %>% tiledb_query("WRITE")
-    qry %>%
-        tiledb_query_set_layout("ROW_MAJOR") %>%  # also default, transpose if COL_MAJOR
-        tiledb_query_set_buffer("a", data) %>%
-        tiledb_query_submit() %>%
+    qry <- tiledb_array(uri = uri) |> tiledb_query("WRITE")
+    qry |>
+        tiledb_query_set_layout("ROW_MAJOR") |>  # also default, transpose if COL_MAJOR
+        tiledb_query_set_buffer("a", data) |>
+        tiledb_query_submit() |>
         tiledb_query_finalize()
     stopifnot(tiledb_query_status(qry)=="COMPLETE")
 }
@@ -121,9 +121,29 @@ read_via_query_object <- function(array_name) {
   print(data.frame(rows=rows,cols=cols,a=values)[1:n,])
 }
 
+read_via_query_piped <- function(array_name) {
+  arr <- tiledb_array(uri)
+
+  rows <- integer(16)
+  cols <- integer(16)
+  values <- integer(16)
+  qry <- tiledb_query(arr, "READ") |>
+    tiledb_query_set_buffer("rows", rows) |>
+    tiledb_query_set_buffer("cols", cols) |>
+    tiledb_query_set_buffer("a", values) |>
+    tiledb_query_set_subarray(c(1L, 4L, 1L, 4L)) |>
+    tiledb_query_submit() |>
+    tiledb_query_finalize()
+  stopifnot(tiledb_query_status(qry) =="COMPLETE")
+
+  n <- tiledb_query_result_buffer_elements(qry, "a")
+  print(data.frame(rows=rows,cols=cols,a=values)[1:n,])
+}
+
 create_array(uri)
 write_array(uri)
 write_array_via_query(uri)
 write_array_via_query_piped(uri)
 read_array(uri)
 read_via_query_object(uri)
+read_via_query_piped(uri)

inst/examples/quickstart_dense_memfs.R

@@ -0,0 +1,147 @@
+
+# quickstart_dense.R
+#
+# LICENSE
+#
+# The MIT License
+#
+# Copyright (c) 2018-2021 TileDB, Inc.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# DESCRIPTION
+#
+# This is a part of the TileDB quickstart tutorial:
+#   https://docs.tiledb.io/en/latest/quickstart.html
+#
+# When run, this program will create a simple 2D dense array, write some data
+# to it, and read a slice of the data back.
+#
+
+library(tiledb)
+
+# Name of the array to create using the in-memory filesystem
+uri <- "mem://quickstart_dense"
+
+create_array <- function(uri) {
+    # Check if the array already exists.
+    if (tiledb_object_type(uri) == "ARRAY") {
+        message("Array already exists, removing to create new one.")
+        tiledb_vfs_remove_dir(uri)
+    }
+
+    # 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")))
+
+    # The array will be dense with a single attribute "a" so each (i,j) cell can store an integer.
+    schema <- tiledb_array_schema(dom, attrs = c(tiledb_attr("a", type = "INT32")))
+
+    # Create the (empty) array on disk.
+    invisible(tiledb_array_create(uri, schema))
+}
+
+write_array <- function(uri) {
+    ## equivalent to matrix(1:16, 4, 4, byrow=TRUE)
+    data <- array(c(c(1L, 5L, 9L, 13L),
+                    c(2L, 6L, 10L, 14L),
+                    c(3L, 7L, 11L, 15L),
+                    c(4L, 8L, 12L, 16L)), dim = c(4,4))
+    # Open the array and write to it.
+    A <- tiledb_array(uri = uri)
+    A[] <- data
+}
+
+write_array_via_query <- function(uri) {
+    data <- 1:16
+    arr <- tiledb_array(uri = uri)
+    qry <- tiledb_query(arr, "WRITE")
+    #qry <- tiledb_query_set_layout(qry, "ROW_MAJOR") # also default, transpose if COL_MAJOR
+    qry <- tiledb_query_set_buffer(qry, "a", data)
+    qry <- tiledb_query_submit(qry)
+    qry <- tiledb_query_finalize(qry)
+    stopifnot(tiledb_query_status(qry)=="COMPLETE")
+}
+
+write_array_via_query_piped <- function(uri) {
+    stopifnot(requireNamespace("magrittr", quietly=TRUE))
+    library(magrittr)
+    data <- 1:16
+    qry <- tiledb_array(uri = uri, "WRITE")
+    qry |>
+        tiledb_query_set_layout("ROW_MAJOR") |>  # also default, transpose if COL_MAJOR
+        tiledb_query_set_buffer("a", data) |>
+        tiledb_query_submit() |>
+        tiledb_query_finalize()
+    stopifnot(tiledb_query_status(qry)=="COMPLETE")
+}
+
+read_array <- function(uri) {
+    # Open the array and read from it.
+    A <- tiledb_array(uri = uri)
+    data <- A[] #A[1:2, 2:4]
+    show(data)
+}
+
+read_via_query_object <- function(array_name) {
+  arr <- tiledb_array(uri)
+  qry <- tiledb_query(arr, "READ")
+
+  rows <- integer(8)
+  cols <- integer(8)
+  values <- integer(8)
+  tiledb_query_set_buffer(qry, "rows", rows)
+  tiledb_query_set_buffer(qry, "cols", cols)
+  tiledb_query_set_buffer(qry, "a", values)
+  tiledb_query_set_subarray(qry, c(1L, 2L, 2L, 4L))
+
+  tiledb_query_submit(qry)
+  tiledb_query_finalize(qry)
+  stopifnot(tiledb_query_status(qry)=="COMPLETE")
+
+  n <- tiledb_query_result_buffer_elements(qry, "a")
+  print(data.frame(rows=rows,cols=cols,a=values)[1:n,])
+}
+
+read_via_query_piped <- function(array_name) {
+  arr <- tiledb_array(uri)
+
+  rows <- integer(16)
+  cols <- integer(16)
+  values <- integer(16)
+  qry <- tiledb_query(arr, "READ") |>
+    tiledb_query_set_buffer("rows", rows) |>
+    tiledb_query_set_buffer("cols", cols) |>
+    tiledb_query_set_buffer("a", values) |>
+    tiledb_query_set_subarray(c(1L, 4L, 1L, 4L)) |>
+    tiledb_query_submit() |>
+    tiledb_query_finalize()
+  stopifnot(tiledb_query_status(qry) =="COMPLETE")
+
+  n <- tiledb_query_result_buffer_elements(qry, "a")
+  print(data.frame(rows=rows,cols=cols,a=values)[1:n,])
+}
+
+create_array(uri)
+write_array(uri)
+write_array_via_query(uri)
+write_array_via_query_piped(uri)
+read_array(uri)
+read_via_query_object(uri)
+read_via_query_piped(uri)