[DRAFT] Generalize unit tests to also allow use against REST CI backend

inst/tinytest/test_aggregates.R

@@ -6,6 +6,13 @@ if (!requireNamespace("palmerpenguins", quietly=TRUE)) exit_file("Remainder need
 
 tiledb_ctx(limitTileDBCores())
 
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) {
+    ## we can rely on the normal tempfile semantics but override the tmpdir
+    ## argument to be our REST CI base url in the unit test namespace
+    tempfile <- function() { base::tempfile(tmpdir="tiledb://unit") }
+}
+
 library(palmerpenguins)
 uri <- tempfile()
 expect_silent(fromDataFrame(penguins, uri, sparse=TRUE))

inst/tinytest/test_arrayschema.R

@@ -1,10 +1,17 @@
 library(tinytest)
 library(tiledb)
 
-isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
 
 ctx <- tiledb_ctx(limitTileDBCores())
 
+
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) {
+    ## we can rely on the normal tempfile semantics but override the tmpdir
+    ## argument to be our REST CI base url in the unit test namespace
+    tempfile <- function() { base::tempfile(tmpdir="tiledb://unit") }
+}
+
 if (get_return_as_preference() != "asis") set_return_as_preference("asis") 		# baseline value
 
 #test_that("tiledb_array_schema default constructor works", {
@@ -97,29 +104,28 @@ expect_error(tiledb:::libtiledb_array_schema_set_capacity(sch@ptr, -10))
 
 
 #test_that("tiledb_array_schema created with encryption",  {
-if (!(isOldWindows)) {
-  dir.create(uri <- tempfile())
-  key <- "0123456789abcdeF0123456789abcdeF"
+if (!isRESTCI) {
+    uri <- tempfile()
+    key <- "0123456789abcdeF0123456789abcdeF"
 
-  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")))
+    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")))
 
-  ##tiledb_array_create_with_key(uri, schema, key)
-  ## for now calling into function
-  tiledb:::libtiledb_array_create_with_key(uri, schema@ptr, key)
+    ##tiledb_array_create_with_key(uri, schema, key)
+    ## for now calling into function
+    tiledb:::libtiledb_array_create_with_key(uri, schema@ptr, key)
 
-#  ctx <- tiledb_ctx()
-#  arrptr <- tiledb:::libtiledb_array_open_with_key(ctx@ptr, uri, "WRITE", key)
-#  A <- new("tiledb_dense", ctx=ctx, uri=uri, as.data.frame=FALSE, ptr=arrptr)
+    ##  ctx <- tiledb_ctx()
+    ##  arrptr <- tiledb:::libtiledb_array_open_with_key(ctx@ptr, uri, "WRITE", key)
+    ##  A <- new("tiledb_dense", ctx=ctx, uri=uri, as.data.frame=FALSE, ptr=arrptr)
 
-#  expect_true(is(A, "tiledb_dense"))
-  ##expect_true(is(schema(A), "tiledb_dense"))
-  ## can't yet read / write as scheme getter not generalized for encryption
+    ##  expect_true(is(A, "tiledb_dense"))
+    ##expect_true(is(schema(A), "tiledb_dense"))
+    ## can't yet read / write as scheme getter not generalized for encryption
 
-  unlink(uri, recursive=TRUE)
+    unlink(uri, recursive=TRUE)
 }
-#})
 
 #test_that("tiledb_array_schema dups setter/getter",  {
 dom <- tiledb_domain(dims = c(tiledb_dim("rows", c(1L, 4L), 4L, "INT32"),

inst/tinytest/test_arrayschemaevolution.R

@@ -1,11 +1,17 @@
 library(tinytest)
 library(tiledb)
 
-#isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
 if (Sys.info()[["sysname"]] == "Windows") exit_file("Skip on Windows")
 
 ctx <- tiledb_ctx(limitTileDBCores())
 
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) {
+    ## we can rely on the normal tempfile semantics but override the tmpdir
+    ## argument to be our REST CI base url in the unit test namespace
+    tempfile <- function() { base::tempfile(tmpdir="tiledb://unit") }
+}
+
 if (tiledb_version(TRUE) < "2.11.0") exit_file("Needs TileDB 2.11.* or later")
 
 df <- data.frame(key=letters[1:10],

inst/tinytest/test_arrowio.R

@@ -1,16 +1,19 @@
 library(tinytest)
 library(tiledb)
 
-isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
-if (isOldWindows) exit_file("skip this file on old Windows releases")
-
 if (Sys.getenv("CI", "") == "") exit_file("Skip unextended test run")
 
 ctx <- tiledb_ctx(limitTileDBCores())
-
 if (!requireNamespace("arrow", quietly=TRUE)) exit_file("No 'arrow' package.")
 suppressMessages(library(arrow))
 
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) {
+    ## we can rely on the normal tempfile semantics but override the tmpdir
+    ## argument to be our REST CI base url in the unit test namespace
+    tempfile <- function() { base::tempfile(tmpdir="tiledb://unit") }
+}
+
 
 if (get_return_as_preference() != "asis") set_return_as_preference("asis") 		# baseline value
 
@@ -40,7 +43,7 @@ tiledb_arrow_array_del(aa)
 ## round-turn test 1: write tiledb first, create arrow object via zero-copy
 suppressMessages(library(bit64))
 n <- 10L
-dir.create(tmp <- tempfile())
+tmp <- tempfile()
 dim <- tiledb_dim("rows", domain=c(1L,n), type="INT32", tile=1L)
 dom <- tiledb_domain(dim)
 sch <- tiledb_array_schema(dom,
@@ -111,7 +114,7 @@ for (col in c("int8", "uint8", "int16", "uint16", "int32", "uint32", "int64", "u
 
 ## n=15
 ## round-turn test 2: create arrow object, write tiledb second via zero-copy
-dir.create(tmp <- tempfile())
+tmp <- tempfile()
 n <- 10L
 
 ## create a schema but don't fill it yet

inst/tinytest/test_attr.R

@@ -3,9 +3,15 @@ library(tiledb)
 
 ctx <- tiledb_ctx(limitTileDBCores())
 
-isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
 isWindows <- Sys.info()[["sysname"]] == "Windows"
 
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) {
+    ## we can rely on the normal tempfile semantics but override the tmpdir
+    ## argument to be our REST CI base url in the unit test namespace
+    tempfile <- function() { base::tempfile(tmpdir="tiledb://unit") }
+}
+
 #test_that("tiledb_attr constructor works", {
 a1 <- tiledb_attr(type = "FLOAT64")
 expect_true(is(a1, "tiledb_attr"))
@@ -54,7 +60,6 @@ expect_true(is.na(tiledb::cell_val_num(attrs)))
 #})
 
 #test_that("tiledb_attr set fill", {
-if (isOldWindows) exit_file("skip remainder of this file on old Windows releases")
 
 ## test for default
 dom <- tiledb_domain(dims = tiledb_dim("rows", c(1L, 4L), 4L, "INT32"))
@@ -238,7 +243,7 @@ expect_equal(D, res)
 
 
 ## lower-level testing tiledb_query_set_buffer
-if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+uri <- tempfile()
 v <- D[, "val"]
 v[3] <- TRUE                            # without nullable for simplicity
 dim <- tiledb_dim(name = "dim", domain = c(0L, 3L), type = "INT32")

inst/tinytest/test_ctx.R

@@ -1,9 +1,6 @@
 library(tinytest)
 library(tiledb)
 
-isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
-if (isOldWindows) exit_file("skip this file on old Windows releases")
-
 tiledb_ctx(limitTileDBCores())
 
 #test_that("tiledb_ctx default constructor", {

inst/tinytest/test_dataframe.R

@@ -1,11 +1,15 @@
 library(tinytest)
 library(tiledb)
 
-isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
-if (isOldWindows) exit_file("skip this file on old Windows releases")
-
 ctx <- tiledb_ctx(limitTileDBCores())
 
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) {
+    ## we can rely on the normal tempfile semantics but override the tmpdir
+    ## argument to be our REST CI base url in the unit test namespace
+    tempfile <- function() { base::tempfile(tmpdir="tiledb://unit") }
+}
+
 #test_that("tiledb_fromdataframe", {
 uri <- tempfile()
 ## turn factor into character
@@ -84,7 +88,7 @@ expect_equal(df, chk[,-1])              # omit first col which is added
 
 if (tiledb_version(TRUE) < "2.1.0") exit_file("Remaining tests require TileDB 2.1.0 or later")
 
-if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+uri <- tempfile()
 fromDataFrame(df, uri, col_index=1)
 arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
@@ -93,7 +97,7 @@ expect_equal(df[,2], na.omit(chk)[,2])  # compare column by column
 expect_equal(df[,3], na.omit(chk)[,3])
 
 
-if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+uri <- tempfile()
 fromDataFrame(df, uri, col_index="index")
 arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
@@ -106,7 +110,7 @@ olddf <- df
 df <- data.frame(chars=olddf$chars,
                  index=olddf$index,     # index not in first column
                  val=olddf$vals)
-if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+uri <- tempfile()
 fromDataFrame(df, uri)
 arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
@@ -116,15 +120,15 @@ if (getRversion() < '4.0.0') {
 }
 expect_equal(df, chk[,-1])              # omit first col which is added
 
-if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+uri <- tempfile()
 fromDataFrame(df, uri, col_index=2)
 arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
 if (getRversion() < '4.0.0') chk$chars <- as.character(chk$chars)
 expect_equal(df[,1], na.omit(chk)[,2])  # compare column by column
 expect_equal(df[,3], na.omit(chk)[,3])
 
-if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+uri <- tempfile()
 fromDataFrame(df, uri, col_index="index")
 arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
@@ -154,14 +158,14 @@ df <- data.frame(time=round(Sys.time(), "secs") + trunc(cumsum(runif(nobs)*3600)
                  nanotime=as.nanotime(Sys.time() + cumsum(runif(nobs)*3600)),
                  stringsAsFactors=FALSE)
 
-if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+uri <- tempfile()
 fromDataFrame(df, uri, sparse=TRUE)
 
 chk <- tiledb_array(uri, return_as="data.frame", extended=FALSE)
 expect_equivalent(df, chk[])            # skip attribute
 
 for (i in seq_len(dim(df)[2])) {
-    if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+    uri <- tempfile()
     fromDataFrame(df, uri, sparse=TRUE, col_index=i)
     chk <- tiledb_array(uri, return_as="data.frame")
     expect_equal(df, chk[][,colnames(df)]) 		# index col comes first so need re-order
@@ -181,17 +185,16 @@ df <- data.frame(time = round(Sys.time(), "secs") + trunc(cumsum(runif(nobs)*360
                  stringsAsFactors=FALSE)
 
 
-if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+uri <- tempfile()
 fromDataFrame(df, uri, sparse=TRUE)
 
 chk <- tiledb_array(uri, return_as="data.frame", extended=FALSE)
 newdf <- chk[]
 if (getRversion() < '4.0.0') newdf$txt <- as.character(newdf$txt)
 expect_equivalent(df, newdf)            # skip attribute
 
-
 for (i in seq_len(dim(df)[2])) {
-    if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+    uri <- tempfile()
     fromDataFrame(df, uri, sparse=TRUE, col_index=i)
     chk <- tiledb_array(uri, return_as="data.frame")
     newdf <- chk[]
@@ -201,14 +204,14 @@ for (i in seq_len(dim(df)[2])) {
 
 combinations <- list(c(1,2), c(1,3), c(2,4), c(3,5), c(4,5), c(2,3,4))
 for (comb in combinations) {
-    if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+    uri <- tempfile()
     fromDataFrame(df, uri, sparse=TRUE, col_index=comb) # by index
     chk <- tiledb_array(uri, return_as="data.frame")
     newdf <- chk[]
     if (getRversion() < '4.0.0') newdf$txt <- as.character(newdf$txt)
     expect_equal(df, newdf[][, colnames(df)])
 
-    if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+    uri <- tempfile()
     fromDataFrame(df, uri, sparse=TRUE, col_index=colnames(df)[comb]) # by name
     chk <- tiledb_array(uri, return_as="data.frame")
     newdf <- chk[]
@@ -292,7 +295,6 @@ library(palmerpenguins)
 data <- penguins
 
 uri <- tempfile()
-
 fromDataFrame(data, uri, col_index=1:2, mode="schema_only")
 arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]
@@ -305,7 +307,7 @@ chk <- arr[]
 expect_equal(nrow(chk), nrow(data))     # all data
 expect_equal(ncol(chk), ncol(data))     # all columns
 
-tiledb_vfs_remove_dir(uri)
+uri <- tempfile()
 fromDataFrame(data, uri, col_index=1:2) # default mode
 arr <- tiledb_array(uri, return_as="data.frame")
 chk <- arr[]

inst/tinytest/test_datetime.R

@@ -1,13 +1,17 @@
 library(tinytest)
 library(tiledb)
 
-isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
-if (isOldWindows) exit_file("skip this file on old Windows releases")
-
 isMacOS <- (Sys.info()['sysname'] == "Darwin")
 
 ctx <- tiledb_ctx(limitTileDBCores())
 
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) {
+    ## we can rely on the normal tempfile semantics but override the tmpdir
+    ## argument to be our REST CI base url in the unit test namespace
+    tempfile <- function() { base::tempfile(tmpdir="tiledb://unit") }
+}
+
 #test_that("Can read / write a simple Date dense vector", {
 uri <- tempfile()
 

inst/tinytest/test_dim.R

@@ -1,11 +1,15 @@
 library(tinytest)
 library(tiledb)
 
-isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
-if (isOldWindows) exit_file("skip this file on old Windows releases")
-
 ctx <- tiledb_ctx(limitTileDBCores())
 
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) {
+    ## we can rely on the normal tempfile semantics but override the tmpdir
+    ## argument to be our REST CI base url in the unit test namespace
+    tempfile <- function() { base::tempfile(tmpdir="tiledb://unit") }
+}
+
 #test_that("tiledb_dim default constructor", {
 dim <- tiledb_dim("foo", c(1, 100))
 expect_true(is(dim, "tiledb_dim"))
@@ -92,7 +96,6 @@ suppressMessages({
 })
 atttype <- "INT32"
 intmax <- .Machine$integer.max         # shorthand
-uri <- tempfile()
 dimtypes <- c("ASCII",  		# Variable length string
               "INT8",   		# 8-bit integer
               "UINT8",  		# 8-bit unsigned integer
@@ -119,7 +122,7 @@ dimtypes <- c("ASCII",  		# Variable length string
               "DATETIME_AS"     # attosecond
               )
 for (dtype in dimtypes) {
-    if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+    uri <- tempfile()
     dom <- switch(dtype,
                   "ASCII"          = NULL,
                   "INT8"           =,
@@ -287,7 +290,7 @@ dimtypes <- c("ASCII",  		# Variable length string
               "DATETIME_AS"     # attosecond
               )
 for (dtype in dimtypes) {
-    if (dir.exists(uri)) unlink(uri, recursive=TRUE)
+    uri <- tempfile()
     dom <- switch(dtype,
                   "ASCII"          = NULL,
                   "INT8"           =,