Second batch of tests

TileDB-Inc · Jan 5, 2024 · aa1b124 · aa1b124
1 parent f074238
commit aa1b124
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Showing 21 changed files with 167 additions and 126 deletions.
diff --git a/inst/tinytest/test_dim.R b/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"           =,

diff --git a/inst/tinytest/test_dimsubset.R b/inst/tinytest/test_dimsubset.R
@@ -5,18 +5,22 @@ library(tinytest)
 library(tiledb)
 library(RcppSpdlog)                     # use logging for some informal profiling
 
-isOldWindows <- Sys.info()[["sysname"]] == "Windows" && grepl('Windows Server 2008', osVersion)
-if (isOldWindows) exit_file("skip this file on old Windows releases")
-
 if (!requireNamespace("nycflights13", quietly=TRUE)) exit_file("Needed 'nycflights13' package missing")
 
+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") }
+}
+
 log_setup("test_dimsubset", "warn")     # but set the default level to 'warn' -> silent, activate via 'info'
 ctx <- tiledb_ctx(limitTileDBCores())
 log_info("ctx created")
 
 op <- options()
 options(stringsAsFactors=FALSE)       # accomodate R 3.*
-dir.create(tmp <- tempfile())
+tmp <- tempfile()
 
 library(nycflights13)
 

diff --git a/inst/tinytest/test_domain.R b/inst/tinytest/test_domain.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_domain basic constructor", {
 d1  <- tiledb_dim("d1", c(1L, 100L))
 dom <- tiledb_domain(list(d1))

diff --git a/inst/tinytest/test_filestore.R b/inst/tinytest/test_filestore.R
@@ -1,13 +1,13 @@
 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")
-
 isWindows <- Sys.info()[["sysname"]] == "Windows"
 
 ctx <- tiledb_ctx(limitTileDBCores())
 
+isRESTCI <- Sys.getenv("TILEDB_CLOUD_REST_BIN", "") != ""
+if (isRESTCI) exit_file("Skipping during REST CI")
+
 if (tiledb_version(TRUE) < "2.9.0") exit_file("Needs TileDB 2.9.* or later")
 
 text_file <- tempfile()

diff --git a/inst/tinytest/test_filter.R b/inst/tinytest/test_filter.R
@@ -1,11 +1,11 @@
 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) exit_file("Skipping during REST CI")
+
 #test_that("tiledb_filter default constructor", {
 flt <- tiledb_filter()
 expect_true(is(flt, "tiledb_filter"))

diff --git a/inst/tinytest/test_filterlist.R b/inst/tinytest/test_filterlist.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")
-
 ctx <- tiledb_ctx(limitTileDBCores())
 
 #test_that("tiledb_filter_list default constructor", {

diff --git a/inst/tinytest/test_fragmentinfo.R b/inst/tinytest/test_fragmentinfo.R
@@ -1,14 +1,18 @@
 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") }
+}
+
 uri <- tempfile()
-if (dir.exists(uri)) unlink(uri, TRUE)
 
 ## create simple array
 set.seed(123)
@@ -61,6 +65,8 @@ D2 <- data.frame(keys = 11:20,
 arr <- tiledb_array(uri, "WRITE")
 arr[] <- D2
 
+if (isRESTCI) exit_file("Skip consolidation during REST CI")
+
 array_consolidate(uri)                  # written twice so consolidate
 
 rm(fraginf)

diff --git a/inst/tinytest/test_group.R b/inst/tinytest/test_group.R
@@ -1,20 +1,25 @@
 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")
 isWindows <- Sys.info()[["sysname"]] == "Windows"
 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") }
+}
+
 if (tiledb_version(TRUE) < "2.8.0") exit_file("TileDB Group requires TileDB 2.8.* or later")
 
 uri <- tempfile()
 
 chk <- tiledb_group_create(uri)
 expect_equal(chk, uri)           # returns uri
-expect_true(dir.exists(chk))
+if (!isRESTCI) expect_true(dir.exists(chk))
 
 ## instantiate and check properties
 grp <- tiledb_group(uri)
@@ -86,11 +91,13 @@ grp <- tiledb_group_close(grp)
 #expect_equal(tiledb_group_metadata_num(grp2), 2)
 #expect_false(tiledb_group_has_metadata(grp2, "otherkey"))
 
+if (isRESTCI) exit_file("skip remainder")   # TODO should this work? Getting 'unrecognised array'
 ## create some temp arrays to adds as groups
 uri1 <- file.path(uri, "anny")
 uri2 <- file.path(uri, "bob")
 uri3 <- file.path(uri, "chloe")
 uri4 <- file.path(uri, "dave")
+
 df1 <- data.frame(val=seq(100, 200, by=10))
 df2 <- data.frame(letters=letters)
 df3 <- data.frame(nine=rep(9L, 9))
@@ -100,7 +107,7 @@ tiledb::fromDataFrame(df2, uri2)
 tiledb::fromDataFrame(df3, uri3)
 tiledb::fromDataFrame(df4, uri4)
 
-## add member
+## add member (unless REST CI)
 grp <- tiledb_group_open(grp, "WRITE")
 grp <- tiledb_group_add_member(grp, uri1, FALSE) 					# use absolute URL
 grp <- tiledb_group_close(grp)

diff --git a/inst/tinytest/test_libtiledb.R b/inst/tinytest/test_libtiledb.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")
-
 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("version is valid", {
 ver <- tiledb_version()
 expect_equal(length(ver), 3)
@@ -33,13 +37,11 @@ expect_equal(unname(tiledb:::libtiledb_config_get(config, "don't exist")), NA_ch
 #})
 
 #test_that("construct libtiledb_config with an empty vector of paramters", {
-params = c()
+params <- c()
 default_config <- tiledb:::libtiledb_config()
 params_config <- tiledb:::libtiledb_config(params)
-expect_equal(
-  tiledb:::libtiledb_config_get(default_config, "sm.tile_cache_size"),
-  tiledb:::libtiledb_config_get(params_config, "sm.tile_cache_size")
-)
+expect_equal(tiledb:::libtiledb_config_get(default_config, "sm.tile_cache_size"),
+             tiledb:::libtiledb_config_get(params_config, "sm.tile_cache_size"))
 #})
 
 #test_that("tiledb_config can be converted to an R vector", {
@@ -92,7 +94,7 @@ dim <- tiledb:::libtiledb_dim(ctx, "d1", "FLOAT64", c(1.0, 100.0), 10.0)
 expect_true(is(dim, "externalptr"))
 #})
 
-
+# n=161
 #test_that("basic libtiledb_domain constructor works", {
 ##ctx <- tiledb:::libtiledb_ctx()
 ctx <- tiledb_get_context()@ptr
@@ -120,6 +122,7 @@ attr <- tiledb:::libtiledb_attribute(ctx, "a1", "INT32", filter_list, 1, FALSE)
 expect_true(is(attr, "externalptr"))
 #})
 
+## n=164
 #test_that("basic float64 libtiledb_attr constructor works", {
 ##ctx <- tiledb:::libtiledb_ctx()
 ctx <- tiledb_get_context()@ptr
@@ -143,7 +146,7 @@ expect_true(is(sch, "externalptr"))
 #})
 
 #test_that("basic dense vector libtiledb_array creation works", {
-dir.create(tmp <- tempfile())
+tmp <- tempfile()
 ##ctx <- tiledb:::libtiledb_ctx()
 ctx <- tiledb_get_context()@ptr
 dim <- tiledb:::libtiledb_dim(ctx, "d1", "INT32", c(1L, 3L), 3L)
@@ -152,14 +155,13 @@ filter <- tiledb:::libtiledb_filter(ctx, "NONE")
 filter_list <- tiledb:::libtiledb_filter_list(ctx, c(filter))
 att <- tiledb:::libtiledb_attribute(ctx, "a1", "FLOAT64", filter_list, 1, FALSE)
 sch <- tiledb:::libtiledb_array_schema(ctx, dom, c(att), cell_order = "COL_MAJOR", tile_order = "COL_MAJOR", sparse = FALSE)
-pth <- paste(tmp, "test_array", sep = "/")
-uri <- tiledb:::libtiledb_array_create(pth, sch)
-expect_true(dir.exists(pth))
+uri <- tiledb:::libtiledb_array_create(tmp, sch)
+if (!isRESTCI) expect_true(dir.exists(tmp))
 unlink(tmp, recursive = TRUE)
 #})
 
 #test_that("basic dense vector writes / reads works", {
-dir.create(tmp <- tempfile())
+tmp <- tempfile()
 ##ctx <- tiledb:::libtiledb_ctx()
 ctx <- tiledb_get_context()@ptr
 dim <- tiledb:::libtiledb_dim(ctx, "d1", "INT32", c(1L, 3L), 3L)
@@ -168,8 +170,7 @@ filter <- tiledb:::libtiledb_filter(ctx, "NONE")
 filter_list <- tiledb:::libtiledb_filter_list(ctx, c(filter))
 att <- tiledb:::libtiledb_attribute(ctx, "a1", "FLOAT64", filter_list, 1, FALSE)
 sch <- tiledb:::libtiledb_array_schema(ctx, dom, c(att), cell_order = "COL_MAJOR", tile_order = "COL_MAJOR", sparse = FALSE)
-pth <- paste(tmp, "test_dense_read_write", sep = "/")
-uri <- tiledb:::libtiledb_array_create(pth, sch)
+uri <- tiledb:::libtiledb_array_create(tmp, sch)
 
 dat <- c(3, 2, 1)
 arr <- tiledb:::libtiledb_array_open(ctx, uri, "WRITE")
@@ -190,7 +191,7 @@ unlink(tmp, recursive = TRUE)
 #})
 
 #test_that("basic dense vector read subarray works", {
-dir.create(tmp <- tempfile())
+tmp <- tempfile()
 ##ctx <- tiledb:::libtiledb_ctx()
 ctx <- tiledb_get_context()@ptr
 dim <- tiledb:::libtiledb_dim(ctx, "d1", "INT32", c(1L, 3L), 3L)
@@ -199,8 +200,7 @@ filter <- tiledb:::libtiledb_filter(ctx, "NONE")
 filter_list <- tiledb:::libtiledb_filter_list(ctx, c(filter))
 att <- tiledb:::libtiledb_attribute(ctx, "a1", "FLOAT64", filter_list, 1, FALSE)
 sch <- tiledb:::libtiledb_array_schema(ctx, dom, c(att), cell_order = "COL_MAJOR", tile_order = "COL_MAJOR", sparse = FALSE)
-pth <- paste(tmp, "test_dense_read_write", sep = "/")
-uri <- tiledb:::libtiledb_array_create(pth, sch)
+uri <- tiledb:::libtiledb_array_create(tmp, sch)
 
 dat <- c(3, 2, 1)
 arr <- tiledb:::libtiledb_array_open(ctx, uri, "WRITE")
@@ -222,6 +222,9 @@ expect_equal(res, dat[sub])
 unlink(tmp, recursive = TRUE)
 #})
 
+if (isRESTCI) exit_file("skip VFS tests")
+
+## n=170
 #test_that("basic tiledb vfs constructor works", {
 ##ctx <- tiledb:::libtiledb_ctx()
 ctx <- tiledb_get_context()@ptr
@@ -234,25 +237,21 @@ expect_true(is(vfs, "externalptr"))
 #})
 
 #test_that("basic vfs is_dir, is_file functionality works", {
-dir.create(tmp <- tempfile())
+tmp <- tempfile()
 
 ##ctx <- tiledb:::libtiledb_ctx()
 ctx <- tiledb_get_context()@ptr
 vfs <- tiledb:::libtiledb_vfs(ctx)
 
 ## test dir
-expect_true(tiledb:::libtiledb_vfs_is_dir(vfs, tmp))
+expect_false(tiledb:::libtiledb_vfs_is_dir(vfs, tmp))
 expect_false(tiledb:::libtiledb_vfs_is_dir(vfs, "i don't exist"))
 
-test_file_path <- paste("file:/", tmp, "test_file", sep = "/")
-test_file <- file(test_file_path, "wb")
+test_file <- file(tmp, "wb")
 writeChar(c("foo", "bar", "baz"), test_file)
 close(test_file)
 
 ## test file
-if(.Platform$OS.type != "windows") {
-  expect_true(tiledb:::libtiledb_vfs_is_file(vfs, test_file_path))
-}
-expect_false(tiledb:::libtiledb_vfs_is_file(vfs, tmp))
+expect_true(tiledb:::libtiledb_vfs_is_file(vfs, tmp))
 unlink(tmp, recursive = TRUE)
 #})
diff --git a/inst/tinytest/test_matrix.R b/inst/tinytest/test_matrix.R
@@ -2,11 +2,15 @@
 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") }
+}
+
 uri <- tempfile()
 M <- matrix(1:16, 4, 4, dimnames=list(LETTERS[1:4], letters[1:4]))
 fromMatrix(M, uri)