File add/removes for bulk-sync from main to release-1.15 (#3258)

* apis/r/tests/testthat/test-contexts.R * two removes
single-cell-data · Oct 29, 2024 · 7b8190c · 7b8190c
1 parent 0ddfb3c
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diff --git a/apis/python/tests/test_util_tiledb.py b/apis/python/tests/test_util_tiledb.py
diff --git a/apis/r/tests/testthat/test-contexts.R b/apis/r/tests/testthat/test-contexts.R
@@ -0,0 +1,216 @@
+test_that("context-create", {
+  skip_if(!extended_tests() || covr_tests())
+
+  uri <- tempfile("new-group")
+  ctx <- soma_context()
+  group <- TileDBGroup$new(
+    uri,
+    internal_use_only = "allowed_use",
+    soma_context = ctx
+  )
+  group$create(internal_use_only = "allowed_use")
+  group$close()
+
+  # Create array and subgroup in isolation but do not yet add them to the group
+  a1 <- TileDBArray$new(
+    uri = create_empty_test_array(file.path(uri, "a1")),
+    internal_use_only = "allowed_use",
+    soma_context = ctx
+  )
+  g1 <- TileDBGroup$new(
+    uri = tiledb::tiledb_group_create(file.path(uri, "g1")),
+    internal_use_only = "allowed_use",
+    soma_context = ctx
+  )
+
+  # Objects are present but not yet members
+  group$open(mode = "READ", internal_use_only = "allowed_use")
+  expect_true(a1$exists())
+  expect_true(g1$exists())
+  expect_equal(group$length(), 0)
+  group$close()
+
+  # Add array and subgroup as members
+  group$open(mode = "WRITE", internal_use_only = "allowed_use")
+  group$set(a1, name = "a1")
+  expect_equal(group$length(), 1)
+  expect_equal(group$to_data_frame()$type, "ARRAY")
+
+  group$set(g1, name = "g1")
+  expect_equal(group$length(), 2)
+  expect_setequal(group$to_data_frame()$type, c("ARRAY", "GROUP"))
+  group$close()
+
+  # Read back the members
+  group$open(mode = "READ", internal_use_only = "allowed_use")
+  expect_equal(group$length(), 2)
+  expect_setequal(group$names(), c("a1", "g1"))
+
+  # Retrieve
+  o <- group$get("a1")
+
+  expect_is(group$get("a1"), "TileDBArray")
+  expect_is(group$get("g1"), "TileDBGroup")
+  group$close()
+
+  # Remove
+  group$open(mode = "WRITE", internal_use_only = "allowed_use")
+  group$remove("a1")
+  expect_equal(group$length(), 1)
+  group$remove("g1")
+  expect_equal(group$length(), 0)
+  group$close()
+
+  # Remove
+  group$open(mode = "READ", internal_use_only = "allowed_use")
+  expect_equal(group$length(), 0)
+  group$close()
+})
+
+test_that("context-fly", {
+  skip_if(!extended_tests() || covr_tests())
+
+  uri <- tempfile("new-group")
+  group <- TileDBGroup$new(
+    uri,
+    internal_use_only = "allowed_use",
+    soma_context = soma_context()
+  )
+  group$create(internal_use_only = "allowed_use")
+  group$close()
+
+  # Create array and subgroup in isolation but do not yet add them to the group
+  a1 <- TileDBArray$new(
+    uri = create_empty_test_array(file.path(uri, "a1")),
+    internal_use_only = "allowed_use",
+    soma_context = soma_context()
+  )
+  g1 <- TileDBGroup$new(
+    uri = tiledb::tiledb_group_create(file.path(uri, "g1")),
+    internal_use_only = "allowed_use",
+    soma_context = soma_context()
+  )
+
+  # Objects are present but not yet members
+  group$open(mode = "READ", internal_use_only = "allowed_use")
+  expect_true(a1$exists())
+  expect_true(g1$exists())
+  expect_equal(group$length(), 0)
+  group$close()
+
+  # Add array and subgroup as members
+  group$open(mode = "WRITE", internal_use_only = "allowed_use")
+  group$set(a1, name = "a1")
+  expect_equal(group$length(), 1)
+  expect_equal(group$to_data_frame()$type, "ARRAY")
+
+  group$set(g1, name = "g1")
+  expect_equal(group$length(), 2)
+  expect_setequal(group$to_data_frame()$type, c("ARRAY", "GROUP"))
+  group$close()
+
+  # Read back the members
+  group$open(mode = "READ", internal_use_only = "allowed_use")
+  expect_equal(group$length(), 2)
+  expect_setequal(group$names(), c("a1", "g1"))
+
+  # Retrieve
+  o <- group$get("a1")
+
+  expect_is(group$get("a1"), "TileDBArray")
+  expect_is(group$get("g1"), "TileDBGroup")
+  group$close()
+
+  # Remove
+  group$open(mode = "WRITE", internal_use_only = "allowed_use")
+  group$remove("a1")
+  expect_equal(group$length(), 1)
+  group$remove("g1")
+  expect_equal(group$length(), 0)
+  group$close()
+
+  # Remove
+  group$open(mode = "READ", internal_use_only = "allowed_use")
+  expect_equal(group$length(), 0)
+  group$close()
+})
+
+test_that("SOMATileDBContext plumb-through", {
+  skip_if(!extended_tests())
+
+  uri <- tempfile("new-group")
+  ctx <- SOMATileDBContext$new()
+
+  expect_no_condition(group <- TileDBGroup$new(
+    uri,
+    internal_use_only = "allowed_use",
+    tiledbsoma_ctx = ctx
+  ))
+  group$create(internal_use_only = "allowed_use")
+  group$close()
+
+  uri <- tempfile("new-group")
+  expect_warning(group <- TileDBGroup$new(
+    uri,
+    internal_use_only = "allowed_use",
+    tiledbsoma_ctx = ctx,
+    soma_context = soma_context()
+  ))
+  group$create(internal_use_only = "allowed_use")
+  group$close()
+})
+
+test_that("Existence proof: soma_context()", {
+  skip_if(!extended_tests() || covr_tests())
+  skip_on_ci()
+
+  uri <- "s3://cellxgene-census-public-us-west-2/cell-census/2024-07-01/soma/"
+  expect_s3_class(
+    grp1 <- TileDBGroup$new(uri, internal_use_only = "allowed_use"),
+    class = 'TileDBGroup'
+  )
+  on.exit(grp1$close(), add = TRUE, after = FALSE)
+  expect_error(grp1$names())
+  grp1$close()
+
+  expect_s3_class(
+    grp2 <- TileDBGroup$new(
+      uri,
+      internal_use_only = "allowed_use",
+      soma_context = soma_context(config = c(vfs.s3.region = "us-west-2", vfs.s3.no_sign_request = "true"))
+    ),
+    class = 'TileDBGroup'
+  )
+  on.exit(grp2$close(), add = TRUE, after = FALSE)
+  expect_identical(grp2$mode(), "CLOSED")
+  expect_no_condition(grp2$open(mode = "READ", internal_use_only = "allowed_use"))
+  expect_type(grp2$names(), "character")
+})
+
+test_that("Existence proof: SOMATileDBContext", {
+  skip_if(!extended_tests() || covr_tests())
+  skip_on_ci()
+
+  uri <- "s3://cellxgene-census-public-us-west-2/cell-census/2024-07-01/soma/"
+  expect_s3_class(
+    grp1 <- TileDBGroup$new(uri, internal_use_only = "allowed_use"),
+    class = 'TileDBGroup'
+  )
+  on.exit(grp1$close(), add = TRUE, after = FALSE)
+  expect_error(grp1$names())
+  grp1$close()
+
+  ctx <- SOMATileDBContext$new(config = c(vfs.s3.region = "us-west-2", vfs.s3.no_sign_request = "true"))
+  expect_s3_class(
+    grp2 <- TileDBGroup$new(
+      uri,
+      internal_use_only = "allowed_use",
+      tiledbsoma_ctx = ctx
+    ),
+    class = 'TileDBGroup'
+  )
+  on.exit(grp2$close(), add = TRUE, after = FALSE)
+  expect_identical(grp2$mode(), "CLOSED")
+  expect_no_condition(grp2$open(mode = "READ", internal_use_only = "allowed_use"))
+  expect_type(grp2$names(), "character")
+})
diff --git a/apis/system/tests/test_version_match.py b/apis/system/tests/test_version_match.py