From 44b8c28d5f4315cab58e6190c6bb0e0fc338ca3f Mon Sep 17 00:00:00 2001
From: John Kerl <kerl.john.r@gmail.com>
Date: Wed, 17 Apr 2024 16:26:59 +0000
Subject: [PATCH] Adapt for R

---
 apis/r/R/SOMADenseNDArray.R                   | 28 +++++++++++++------
 apis/r/R/SOMAExperimentAxisQuery.R            | 16 +++++------
 apis/r/tests/testthat/test-SOMADenseNDArray.R |  2 +-
 3 files changed, 29 insertions(+), 17 deletions(-)

diff --git a/apis/r/R/SOMADenseNDArray.R b/apis/r/R/SOMADenseNDArray.R
index 464685de55..bfa32c23e3 100644
--- a/apis/r/R/SOMADenseNDArray.R
+++ b/apis/r/R/SOMADenseNDArray.R
@@ -44,15 +44,18 @@ SOMADenseNDArray <- R6::R6Class(
 
       result_order <- map_query_layout(match_query_layout(result_order))
 
-      if (!is.null(coords)) {
-        coords <- private$.convert_coords(coords)
+      if (is.null(coords)) {
+        # These are 0-up: add 1 for R use
+        ned <- self$non_empty_domain()
+        coords <- lapply(X=as.integer(ned), FUN=function(x){0:x})
       }
+      coords <- private$.convert_coords(coords)
 
       cfg <- as.character(tiledb::config(self$tiledbsoma_ctx$context()))
       rl <- soma_array_reader(uri = uri,
-                              dim_points = coords,        # NULL dealt with by soma_array_reader()
+                              dim_points = coords,
                               result_order = result_order,
-                              loglevel = log_level,       # idem
+                              loglevel = log_level,       # NULL dealt with by soma_array_reader()
                               config = cfg)
 
       soma_array_to_arrow_table(rl)
@@ -74,15 +77,24 @@ SOMADenseNDArray <- R6::R6Class(
 
       dims <- self$dimensions()
       attr <- self$attributes()
+
       stopifnot("Array must have two dimensions" = length(dims) == 2,
-                "Array must contain columns 'soma_dim_0' and 'soma_dim_1'" =
-                    all.equal(c("soma_dim_0", "soma_dim_1"), names(dims)),
                 "Array must contain column 'soma_data'" = all.equal("soma_data", names(attr)))
 
+      if (is.null(coords)) {
+        ned <- self$non_empty_domain()
+        # These are 0-up: add 1 for R use
+        nrow <- as.numeric(ned[[1]]) + 1
+        ncol <- as.numeric(ned[[2]]) + 1
+      } else {
+        nrow <- length(unique(as.numeric(coords[[1]])))
+        ncol <- length(unique(as.numeric(coords[[2]])))
+      }
+
       tbl <- self$read_arrow_table(coords = coords, result_order = result_order, log_level = log_level)
       m <- matrix(as.numeric(tbl$GetColumnByName("soma_data")),
-                  nrow = length(unique(as.numeric(tbl$GetColumnByName("soma_dim_0")))),
-                  ncol = length(unique(as.numeric(tbl$GetColumnByName("soma_dim_1")))),
+                  nrow = nrow,
+                  ncol = ncol,
                   byrow = result_order == "ROW_MAJOR")
 
     },
diff --git a/apis/r/R/SOMAExperimentAxisQuery.R b/apis/r/R/SOMAExperimentAxisQuery.R
index c4a73d3630..d44bb80a83 100644
--- a/apis/r/R/SOMAExperimentAxisQuery.R
+++ b/apis/r/R/SOMAExperimentAxisQuery.R
@@ -425,24 +425,24 @@ SOMAExperimentAxisQuery <- R6::R6Class(
       # reindex the coordinates.
       mat_coords <- switch(collection,
         X = list(
-          i = self$indexer$by_obs(tbl$soma_dim_0),
-          j = self$indexer$by_var(tbl$soma_dim_1)
+          i = self$indexer$by_obs(tbl$soma_dim_0), # XXX UPDATE HERE FOR DENSE
+          j = self$indexer$by_var(tbl$soma_dim_1)  # XXX UPDATE HERE FOR DENSE
         ),
         obsm = list(
-          i = self$indexer$by_obs(tbl$soma_dim_0),
+          i = self$indexer$by_obs(tbl$soma_dim_0), # XXX UPDATE HERE FOR DENSE
           j = tbl$soma_dim_1
         ),
         varm = list(
-          i = self$indexer$by_var(tbl$soma_dim_0),
+          i = self$indexer$by_var(tbl$soma_dim_0), # XXX UPDATE HERE FOR DENSE
           j = tbl$soma_dim_1
         ),
         obsp = list(
-          i = self$indexer$by_obs(tbl$soma_dim_0),
-          j = self$indexer$by_obs(tbl$soma_dim_1)
+          i = self$indexer$by_obs(tbl$soma_dim_0), # XXX UPDATE HERE FOR DENSE
+          j = self$indexer$by_obs(tbl$soma_dim_1)  # XXX UPDATE HERE FOR DENSE
         ),
         varp = list(
-          i = self$indexer$by_var(tbl$soma_dim_0),
-          j = self$indexer$by_var(tbl$soma_dim_1)
+          i = self$indexer$by_var(tbl$soma_dim_0), # XXX UPDATE HERE FOR DENSE
+          j = self$indexer$by_var(tbl$soma_dim_1)  # XXX UPDATE HERE FOR DENSE
         )
       )
 
diff --git a/apis/r/tests/testthat/test-SOMADenseNDArray.R b/apis/r/tests/testthat/test-SOMADenseNDArray.R
index 53f9048952..1eadc8eb01 100644
--- a/apis/r/tests/testthat/test-SOMADenseNDArray.R
+++ b/apis/r/tests/testthat/test-SOMADenseNDArray.R
@@ -21,7 +21,7 @@ test_that("SOMADenseNDArray creation", {
   ndarray <- SOMADenseNDArrayOpen(uri)
   tbl <- ndarray$read_arrow_table(result_order = "COL_MAJOR")
   expect_true(is_arrow_table(tbl))
-  expect_equal(tbl$ColumnNames(), c("soma_dim_0", "soma_dim_1", "soma_data"))
+  expect_equal(tbl$ColumnNames(), c("soma_data"))
 
   expect_identical(
     as.numeric(tbl$GetColumnByName("soma_data")),