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[r] Plumb old-style contexts to new libtiledbsoma contexts (#3252)
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* [r] Plumb old-style contexts to new libtiledbsoma contexts
Allow plumbing tiledb-r contexts `SOMATileDBContext` objects into
libtiledbsoma `soma_context()` objects

Modified SOMA methods:
 - `TileDBObject$new()`: plumb `tiledbsoma_ctx` config options into
   `soma_context()` when provided

[SC-56531](https://app.shortcut.com/tiledb-inc/story/56531)
addresses #3213

* add no-sign-request to S3 test cases

* Update changelog
Bump develop version

---------

Co-authored-by: John Kerl <[email protected]>
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@mojaveazure @johnkerl
mojaveazure and johnkerl authored Oct 29, 2024
1 parent 2be2864 commit 467af01
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2 changes: 1 addition & 1 deletion apis/r/DESCRIPTION
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Expand Up @@ -6,7 +6,7 @@ Description: Interface for working with 'TileDB'-based Stack of Matrices,
like those commonly used for single cell data analysis. It is documented at
<https://github.com/single-cell-data>; a formal specification available is at
<https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md>.
Version: 1.15.99.12
Version: 1.15.99.13
Authors@R: c(
person(given = "Aaron", family = "Wolen",
role = c("cre", "aut"), email = "[email protected]",
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1 change: 1 addition & 0 deletions apis/r/NEWS.md
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Expand Up @@ -20,6 +20,7 @@
* Proper prefixing for shape-related methods [#3237](https://github.com/single-cell-data/TileDB-SOMA/pull/3237)
* Bindings for `upgrade_domain` [#3238](https://github.com/single-cell-data/TileDB-SOMA/pull/3238)
* Apply `styler::style_pkg()` [#3239](https://github.com/single-cell-data/TileDB-SOMA/pull/3239)
* Plumb old-style `SOMATileDBContext` into new-style `soma_context()`

# tiledbsoma 1.14.5

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33 changes: 28 additions & 5 deletions apis/r/R/TileDBObject.R
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Expand Up @@ -39,12 +39,35 @@ TileDBObject <- R6::R6Class(
private$.tiledb_platform_config <- platform_config

# Set context
tiledbsoma_ctx <- tiledbsoma_ctx %||% SOMATileDBContext$new()
if (!inherits(x = tiledbsoma_ctx, what = "SOMATileDBContext")) {
stop("'tiledbsoma_ctx' must be a SOMATileDBContext object", call. = FALSE)
if (!is.null(x = tiledbsoma_ctx)) {
if (!inherits(x = tiledbsoma_ctx, what = 'SOMATileDBContext')) {
stop(
"'tiledbsoma_ctx' must be a SOMATileDBContext object",
call. = FALSE
)
}
# TODO: Deprecate tiledbsoma_ctx in favor of soma_context
# warning("'tiledbsoma_ctx' is deprecated, use 'soma_context' instead")
# Set the old context
private$.tiledbsoma_ctx <- tiledbsoma_ctx
private$.tiledb_ctx <- self$tiledbsoma_ctx$context()
# Also plumb through to the new context
if (!is.null(soma_context)) {
warning(
"Both 'soma_context' and 'tiledbsoma_ctx' were provided,",
"using 'soma_context' only"
)
} else {
# why we named the parameter and function the same thing is beyond me
soma_context <- tiledbsoma::soma_context(
config = unlist(tiledbsoma_ctx$to_list())
)
}
} else {
tiledbsoma_ctx <- SOMATileDBContext$new()
private$.tiledbsoma_ctx <- tiledbsoma_ctx
private$.tiledb_ctx <- self$tiledbsoma_ctx$context()
}
private$.tiledbsoma_ctx <- tiledbsoma_ctx
private$.tiledb_ctx <- self$tiledbsoma_ctx$context()

# TODO: re-enable once new UX is worked out
# soma_context <- soma_context %||% soma_context()
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216 changes: 216 additions & 0 deletions apis/r/tests/testthat/test-contexts.R
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@@ -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")
})

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