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[r] use new SOMATileDBContext$context() accessor #357

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merged 2 commits into from
Apr 6, 2023
Merged

[r] use new SOMATileDBContext$context() accessor #357

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4a33076
[r] use new SOMATileDBContext$context() accessor
mlin Apr 5, 2023
d09788d
bump KNOWN_CENSUS_VERSION
mlin Apr 5, 2023
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2 changes: 1 addition & 1 deletion api/r/cellxgene.census/R/open.R
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ open_soma <- function(census_version = "latest", uri = NULL, tiledbsoma_ctx = NU
} else {
# FIXME: we should use something like SOMATileDBContext$replace() (yet to
# exist) in case the user context has other important fields besides config
cfg <- as.vector(tiledb::config(tiledbsoma_ctx$get_tiledb_context()))
cfg <- as.vector(tiledb::config(tiledbsoma_ctx$context()))
if (!is.null(s3_region)) {
cfg["vfs.s3.region"] <- s3_region
}
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16 changes: 5 additions & 11 deletions api/r/cellxgene.census/R/source_h5ad.R
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Expand Up @@ -19,17 +19,11 @@ get_source_h5ad_uri <- function(dataset_id, census_version = "latest") {
)
)

# FIXME execution of value_filter:
# Error: Currently unsupported type: UTF8
# dataset <- as.data.frame(
# census$get("census_info")$get("datasets")$read(
# value_filter=paste("dataset_id == '", dataset_id, "'", sep="")
# ))
# should replace retrieving the entire datasets dataframe:
dataset <- as.data.frame(census$get("census_info")$get("datasets")$read(
column_names = c("dataset_id", "dataset_h5ad_path")
))
dataset <- dataset[dataset$dataset_id == dataset_id, ]
dataset <- as.data.frame(
census$get("census_info")$get("datasets")$read(
value_filter = paste("dataset_id == '", dataset_id, "'", sep = "")
)
)
stopifnot("Unknown dataset_id" = nrow(dataset) == 1)
dataset <- as.list(dataset[1, ])

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2 changes: 1 addition & 1 deletion api/r/cellxgene.census/tests/testthat/test-release_directory.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# A known-good Cell Census version. This may need updating if the version used
# is withdrawn for any reason.
KNOWN_CENSUS_VERSION <- "2023-02-13"
KNOWN_CENSUS_VERSION <- "2023-04-04"
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Ah! This will be less of a problem once have a LTS (5 year) release.

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Why not just designate one build to be a "long term test build", give it a tag, and not delete it? I don't think we need a "real" LTS release for this purpose....

KNOWN_CENSUS_URI <- paste(
"s3://cellxgene-data-public/cell-census/",
KNOWN_CENSUS_VERSION,
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