[r] Update SOMADataFrame$create() to automatically mark ordered() (…

…#1720)

* [r] Update `SOMADataFrame$create()` to automatically mark `ordered()`
Add an check in `SOMADataFrame$create()` to detect if a column in the schema is ordered. If so, automatically mark the enumerations as such. Note: this only happens if:
- there are enumerations for the column
- the column in the arrow schema is marked as ordered
- there is no attribute `'ordered'` on the enumerations for the column

* name unusual argument

* Bump develop version
Update changelog

apis/r/DESCRIPTION

@@ -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: 1.4.3.1
+Version: 1.4.3.2
 Authors@R: c(
     person(given = "Aaron", family = "Wolen",
            role = c("cre", "aut"), email = "[email protected]",

apis/r/NEWS.md

@@ -4,6 +4,7 @@
 
 * Add support for writing `SummarizedExperiment` and `SingleCellExperiment` object to SOMAs
 * Add support for bounding boxes for sparse arrays
+* Add support for creating `SOMADataFrames` with `ordered()` columns
 
 
 # tiledbsoma 1.4.0

apis/r/R/SOMADataFrame.R

@@ -97,6 +97,11 @@ SOMADataFrame <- R6::R6Class(
         field <- schema$GetFieldByName(field_name)
         field_type <- tiledb_type_from_arrow_type(field$type)
 
+        # Check if the field is ordered and mark it as such
+        if (!is.null(x = levels[[field_name]]) && isTRUE(field$type$ordered)) {
+          attr(levels[[field_name]], 'ordered') <- attr(levels[[field_name]], 'ordered', exact = TRUE) %||% TRUE
+        }
+
         tdb_attrs[[field_name]] <- tiledb::tiledb_attr(
           name = field_name,
           type = field_type,

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

@@ -222,6 +222,76 @@ test_that("int64 values are stored correctly", {
   gc()
 })
 
+test_that("creation with ordered factors", {
+  skip_if_not_installed("tiledb", "0.21.0")
+  skip_if(!extended_tests())
+  uri <- withr::local_tempdir("soma-dataframe-ordered")
+  n <- 10L
+  df <- data.frame(
+    soma_joinid = bit64::as.integer64(seq_len(length.out = n) - 1L),
+    int = seq_len(length.out = n),
+    bool = rep_len(c(TRUE, FALSE), length.out = n),
+    ord = ordered(rep_len(c("g1", "g2", "g3"), length.out = n))
+  )
+  tbl <- arrow::as_arrow_table(df)
+  expect_true(tbl$schema$GetFieldByName("ord")$type$ordered)
+  expect_no_condition(sdf <- SOMADataFrameCreate(
+    uri = uri,
+    schema = tbl$schema,
+    levels = sapply(
+      X = df[, setdiff(names(df), "soma_joinid")],
+      FUN = levels,
+      simplify = FALSE,
+      USE.NAMES = TRUE
+    )
+  ))
+  expect_no_condition(sdf$write(values = tbl))
+  expect_s3_class(sdf <- SOMADataFrameOpen(uri), "SOMADataFrame")
+  expect_true(sdf$schema()$GetFieldByName("ord")$type$ordered)
+  expect_s3_class(ord <- sdf$object[]$ord, c("ordered", "factor"), exact = TRUE)
+  expect_length(ord, n)
+  expect_identical(levels(ord), levels(df$ord))
+})
+
+test_that("explicit casting of ordered factors to regular factors", {
+  skip_if_not_installed("tiledb", "0.21.0")
+  skip_if(!extended_tests())
+  uri <- withr::local_tempdir("soma-dataframe-unordered")
+  n <- 10L
+  df <- data.frame(
+    soma_joinid = bit64::as.integer64(seq_len(length.out = n) - 1L),
+    int = seq_len(length.out = n),
+    bool = rep_len(c(TRUE, FALSE), length.out = n),
+    ord = ordered(rep_len(c("g1", "g2", "g3"), length.out = n))
+  )
+  tbl <- arrow::as_arrow_table(df)
+  expect_true(tbl$schema$GetFieldByName("ord")$type$ordered)
+  lvls <- sapply(
+    X = df[, setdiff(names(df), "soma_joinid")],
+    FUN = levels,
+    simplify = FALSE,
+    USE.NAMES = TRUE
+  )
+  for (col in names(lvls)) {
+    if (!is.null(lvls[[col]])) {
+      attr(lvls[[col]], 'ordered') <- FALSE
+    }
+  }
+  expect_no_condition(sdf <- SOMADataFrameCreate(
+    uri = uri,
+    schema = tbl$schema,
+    levels = lvls
+  ))
+  expect_no_condition(sdf$write(values = tbl))
+  expect_s3_class(sdf <- SOMADataFrameOpen(uri), "SOMADataFrame")
+  expect_false(sdf$schema()$GetFieldByName("ord")$type$ordered)
+  expect_s3_class(ord <- sdf$object[]$ord, "factor", exact = TRUE)
+  expect_false(is.ordered(ord))
+  expect_length(ord, n)
+  expect_identical(levels(ord), levels(df$ord))
+})
+
+
 test_that("SOMADataFrame read", {
   skip_if(!extended_tests())
   uri <- extract_dataset("soma-dataframe-pbmc3k-processed-obs")