Add metadata hints for v5 writing

Expand tests

apis/r/R/utils-seurat.R

@@ -88,6 +88,13 @@
   return(commands[idx])
 }
 
+.assay_version_hint <- function(type = c('v3', 'v5')) {
+  type <- match.arg(type)
+  return(list(soma_ecosystem_seurat_assay_version = type))
+}
+
+.ragged_array_hint <- function() list(soma_ecosystem_seurat_v5_ragged = 'ragged')
+
 .MINIMUM_SEURAT_VERSION <- function(repr = c('v', 'c')) {
   repr <- repr[1L]
   repr <- match.arg(arg = repr)

apis/r/R/write_seurat.R

@@ -259,6 +259,7 @@ write_soma.Assay5 <- function(
     platform_config = platform_config,
     tiledbsoma_ctx = tiledbsoma_ctx
   )
+  ms$set_metadata(.assay_version_hint('v5'))
   X <- if (!'X' %in% ms$names()) {
     SOMACollectionCreate(
       uri = file_path(ms$uri, 'X'),
@@ -327,6 +328,7 @@ write_soma.Assay5 <- function(
       shape = as.integer(shape)
     )
     arr$.__enclos_env__$private$.write_coo_dataframe(coo)
+    arr$set_metadata(.ragged_array_hint())
   }
 
   # Write feature-level meta data

apis/r/tests/testthat/test-SeuratIngest.R

@@ -139,37 +139,52 @@ test_that("Write Assay mechanics", {
 
 test_that("Write v5 in-memory Assay mechanics", {
   skip_if(!extended_tests())
-  skip_if_not_installed('SeuratObject', minimum_version = '5.0.1')
+  skip_if_not_installed("SeuratObject", minimum_version = "5.0.2")
 
-  uri <- withr::local_tempdir("write-v5-assay")
+  uri <- tempfile(pattern = "write-v5-assay")
   collection <- SOMACollectionCreate(uri)
   on.exit(collection$close(), add = TRUE, after = FALSE)
 
-  rna <- get_data('pbmc_small', package = 'SeuratObject')[['RNA']]
-  rna <- as(rna, 'Assay5')
+  rna <- get_data("pbmc_small", package = "SeuratObject")[["RNA"]]
+  rna <- as(rna, "Assay5")
   expect_no_condition(ms <- write_soma(rna, soma_parent = collection))
   expect_s3_class(ms, 'SOMAMeasurement')
   expect_true(ms$exists())
   on.exit(ms$close(), add = TRUE, after = FALSE)
 
-  expect_identical(ms$uri, file.path(collection$uri, 'rna'))
-  expect_identical(ms$names(), c('X', 'var'))
-  expect_s3_class(ms$var, 'SOMADataFrame')
-  expect_identical(setdiff(ms$var$attrnames(), 'var_id'), names(rna[[]]))
-  expect_s3_class(ms$X, 'SOMACollection')
+  expect_identical(ms$uri, file.path(collection$uri, "rna"))
+  assay_hint <- .assay_version_hint("v5")
+  expect_equivalent(
+    ms$get_metadata(names(assay_hint)),
+    assay_hint[[1L]]
+  )
+  expect_identical(ms$names(), c("X", "var"))
+  expect_s3_class(ms$var, "SOMADataFrame")
+  expect_identical(setdiff(ms$var$attrnames(), "var_id"), names(rna[[]]))
+  expect_s3_class(ms$X, "SOMACollection")
   expect_identical(ms$X$names(), SeuratObject::Layers(rna))
-  fmat <- methods::slot(rna, name = 'features')
-  cmat <- methods::slot(rna, name = 'cells')
+  fmat <- methods::slot(rna, name = "features")
+  cmat <- methods::slot(rna, name = "cells")
+  ragged_hint <- .ragged_array_hint()
   for (lyr in SeuratObject::Layers(rna)) {
     idx <- which(cmat[, lyr])
     jdx <- which(fmat[, lyr])
     expect_equal(ms$X$get(lyr)$shape(), c(max(idx), max(jdx)), info = lyr)
+    switch(
+      EXPR = lyr,
+      scale.data = expect_equivalent(
+        ms$X$get(lyr)$get_metadata(names(ragged_hint)),
+        ragged_hint[[1L]],
+        info = lyr
+      ),
+      expect_null(ms$X$get(lyr)$get_metadata(names(ragged_hint)), info = lyr)
+    )
   }
 
   # Test ragged arrays
-  mat <- SeuratObject::LayerData(rna, 'counts')
-  cells2 <- paste0(colnames(rna), '.2')
-  features2 <- paste0(rownames(rna), '.2')
+  mat <- SeuratObject::LayerData(rna, "counts")
+  cells2 <- paste0(colnames(rna), ".2")
+  features2 <- paste0(rownames(rna), ".2")
   layers <- list(
     mat = mat,
     cells2 = `colnames<-`(mat, cells2),
@@ -179,19 +194,24 @@ test_that("Write v5 in-memory Assay mechanics", {
   expect_s4_class(rna2 <- SeuratObject::.CreateStdAssay(layers), "Assay5")
   expect_identical(dim(rna2), dim(rna) * 2)
 
-  expect_no_condition(ms2 <- write_soma(rna2, uri = 'ragged-arrays', soma_parent = collection))
-  expect_s3_class(ms2, 'SOMAMeasurement')
+  expect_no_condition(ms2 <- write_soma(rna2, uri = "ragged-arrays", soma_parent = collection))
+  expect_s3_class(ms2, "SOMAMeasurement")
   expect_true(ms2$exists())
   on.exit(ms2$close(), add = TRUE, after = FALSE)
 
-  expect_identical(ms2$uri, file.path(collection$uri, 'ragged-arrays'))
+  expect_identical(ms2$uri, file.path(collection$uri, "ragged-arrays"))
   expect_identical(ms2$X$names(), SeuratObject::Layers(rna2))
-  fmat <- methods::slot(rna2, name = 'features')
-  cmat <- methods::slot(rna2, name = 'cells')
+  fmat <- methods::slot(rna2, name = "features")
+  cmat <- methods::slot(rna2, name = "cells")
   for (lyr in SeuratObject::Layers(rna2)) {
     idx <- which(cmat[, lyr])
     jdx <- which(fmat[, lyr])
     expect_equal(ms2$X$get(lyr)$shape(), c(max(idx), max(jdx)), info = lyr)
+    expect_equivalent(
+      ms2$X$get(lyr)$get_metadata(names(ragged_hint)),
+      ragged_hint[[1L]],
+      info = lyr
+    )
   }
 })
 
@@ -412,3 +432,41 @@ test_that("Write Seurat mechanics", {
 
   gc()
 })
+
+test_that("Write Seurat with v3 and v5 assays", {
+  skip_if(!extended_tests())
+  skip_if_not_installed("SeuratObject", minimum_version = "5.0.2")
+
+  pbmc_small <- get_data("pbmc_small", package = "SeuratObject")
+  suppressWarnings(pbmc_small[["RNA5"]] <- methods::as(pbmc_small[["RNA"]], "Assay5"))
+  extra <- c(
+    SeuratObject::Graphs(pbmc_small),
+    SeuratObject::Reductions(pbmc_small),
+    SeuratObject::Command(pbmc_small)
+  )
+  for (i in extra) {
+    pbmc_small[[i]] <- NULL
+  }
+
+  assay_hint <- .assay_version_hint("v5")
+  uri <- tempfile(pattern = SeuratObject::Project(pbmc_small))
+
+  expect_no_condition(uri <- write_soma(pbmc_small, uri))
+  expect_type(uri, "character")
+  expect_no_condition(experiment <- SOMAExperimentOpen(uri))
+  on.exit(experiment$close(), add = TRUE, after = FALSE)
+
+  expect_s3_class(experiment, "SOMAExperiment")
+  expect_no_error(experiment$ms)
+  expect_identical(sort(experiment$ms$names()), sort(c("RNA", "RNA5")))
+  for (assay in experiment$ms$names()) {
+    expect_s3_class(experiment$ms$get(assay), "SOMAMeasurement")
+    if (inherits(pbmc_small[[assay]], "Assay5")) {
+      expect_equivalent(
+        experiment$ms$get(assay)$get_metadata(names(assay_hint)),
+        assay_hint[[1L]],
+        info = assay
+      )
+    }
+  }
+})