Repository: single-cell-data/TileDB-SOMA (language: python)

Issue:
[python/r/c++] Revisit `shape` for component arrays
## PRs

**Merged PRs:**

<details>

* #2909 `kerl/schevo-timestamp-methodize`
* #2913 `kerl/name-neaten`
* #2908 `kerl/ut-soma-exc-simplify`
* #2910 `kerl/test-common-parameterize`
* #2918 `kerl/cpp-test-deadstrip`
* #2919 `kerl/minor-unit-test-helper-mod`
* #2936 `kerl/cpp-ut-helper-neaten`
* #2938 `kerl/more-cur-dom-parameterize`
* #2915 `kerl/cpp-strict-int64-shape`
* #2911 `kerl/arrow-util-current-domain-optional`
* #2939 `kerl/step-two-temp`
* #2947 `kerl/cpp-ndarray-resize-testing`
* #2945 `kerl/dataframe-test-fixture`
* #2944 `kerl/cpp-variant-indexed-dataframes`
* #2916 `kerl/sdf-shape`
* #2917 `kerl/cpp-resizes`
* #2948 `kerl/upgrade-shape-int64`
* #2951 `kerl/sdf-test-accessors`
* #2953 `kerl/py-r-accessor-plumbing`
* #2957 `kerl/sdf-domain-accessors`
* #2960 `kerl/dense-link`
* #2963 `kerl/nightly-fix`
* #2970 `kerl/dense-writeable-after-create`
* #2968 `kerl/minor-trim`
* #2969 `kerl/more-py-domain-name-neaten`
* #2972 `kerl/libtiledbsoma-env-logging-level`
* #2962 `kerl/py-r-creation-paths`
* #2950 `kerl/py-r-test-2`
* #2994 `kerl/nanoarrow-helpers`
* #3011 `kerl/polydom3`
* #3017 `kerl/polydom5`
* #3018 `kerl/polydom6`
* #2990 `kerl/variant-nnz-bug`
* #3019 `kerl/index-swap`
* #3020 `kerl/ut-max-shape`
* #3012 `kerl/polydom4`
* #3025 `kerl/fix-3020-merge`
* #3026 `kerl/one-more-rename`
* #3028 `kerl/ff-not`
* #3029 `kerl/ut-vg`
* #3030 `kerl/table-utils-memory`
* #3067 `kerl/improve-sdf-test-field-names`
* #3068 `kerl/ut-generate`
* #3069 `kerl/cpp-sdf-domain-at-create`
* #3027 `kerl/hll-domainish`
* #3088 `kerl/max-domain-int64`
* #3090 `kerl/maybe-resize-soma-joinid-cpp-tweak`
* #3032 `kerl/sdf-domain-at-create` -- fixes #2967
* #3091 `kerl/maybe-resize-soma-joinid-py-r`
* #3095 `kerl/cpp-exp-resize-prep`
* #3089 `kerl/r-dataframe-shapeable`
* https://github.com/single-cell-data/SOMA/pull/233
* #3125 `kerl/cpp-ut-name-shortens`
* #3127 `kerl/helper-rename`
* #3130 `kerl/cpp-can-resizers-names`
* #3132 `kerl/cpp-dataframe-sizing-helpers`
* #3139 `kerl/cpp-dataframe-upgrade-test`
* #3140 `kerl/py-resizer-connects`
* #3151 `kerl/py-can-upgrade-shape`
* #3152 `kerl/registration-shape-acceessors`
* #3156 `kerl/py-exp-shaping`
* #3157 `kerl/py-exp-shaping2`
* #3148 `kerl/py-exp-resize`
* #3191 `kerl/py-domain-at-create-ut-1`
* #3190 `kerl/py-domain-at-create-ut-2`
* #3192 `kerl/py-domain-at-create-ut-3`
* #3193 `kerl/py-domain-at-create-ut-4`
* #3194 `kerl/py-domain-at-create-ut-5`
* #3203 `kerl/min-size-2`
* #3208 `kerl/r-min-sizing`
* #3211 `kerl/cpp-ugr-dom`
* #3232 `kerl/ff-interop`
* #3230 `kerl/ffon`
* #3234 `kerl/docstring-prune`
* #3236 `kerl/prefixing`
* #3241 `kerl/fix-bad-merge`
* #3235 `kerl/py-r-ugr-dom`
* #3237 `kerl/py-r-ugr-dom-2`
* #3238 `kerl/py-r-ugr-dom-3`
* #3253 `kerl/set-coords-rename`
* #3261 `kerl/pybind11-nda-sizing`
* #3265 `kerl/dense-227-a`
* #3263 `kerl/dense-range-trim`
* #3268 `kerl/dim-explosion`
* #3269 `kerl/python-227-dense-ned-read`
* #3270 `kerl/r-227-dense-fixes`
* #3280 `kerl/r-dense-227-more`
* #3286 `kerl/more-fn4m`
* #3283 `kerl/readthedocs-pre-1.15`
* #3288 `kerl/dense-ugrsh`
* #3289 `kerl/notebook-shape-upgrade`
* #3285 `kerl/new-shape-doc-updates`
* #3295 `kerl/notebook-data-refresh`
* #3290 `kerl/notebook-new-shape-refresh`
* #3301 `kerl/ffena`
* #3303 `kerl/r-data-refresh`
* #3300 `kerl/sdf-sjid-lower-zero`
* #3296 `kerl/dense-example-data-refresh`
* #3294 `kerl/new-shape-notebook-and-vignette`
* #3308 `kerl/upgrade-experiment-resources`
* #3309 `kerl/fix-notebook-merge`
* #3321 `kerl/more-use-shape`
* #3358 `kerl/revert-3300`
* #3368 `kerl/227a`
* #3369 `kerl/ucd1`
* #3370 `kerl/ucd2`
* #3371 `kerl/ucd3`
* #3372 `kerl/ucd4`
* #3396 `kerl/domain-at-create-docstrings`
* #3302 `kerl/new-shape-vignette`
* https://github.com/single-cell-data/SOMA/pull/250
* #3399 `kerl/new-shape-more-docstrings`
* #3400 `kerl/check-only-r`
* https://github.com/TileDB-Inc/somacore-feedstock/pull/27

</details>

**Closed/abandoned PRs:**

<details>

* #2785 -- This was only dogfooding for the core 2.25 release -- not to be merged
* #2952 `kerl/feature-flag-temp` -- folded into 2962
* #2995 `kerl/polydom`
* #2964 `kerl/tiledbsoma-io-test`
* #3189 `kerl/min-size`
* #3220 `kerl/cpp-ugr-dom-2`
* #3244 `kerl/dense-227-fixes`
* #3276 `kerl/dataframe-shape`

</details>

**Issues which are related but non-blocking:**

* https://github.com/single-cell-data/SOMA/pull/216
* https://github.com/TileDB-Inc/TileDB/pull/5303
* #2966
* #3081
* Note: R append mode does not exist yet -- see #1630 -- so an experiment-level resizer is not a priority in R
* #3271 
* #3272
* #3273

**See also:** [[sc-51048]](https://app.shortcut.com/tiledb-inc/story/51048).

## Problem to be solved

Users want to know the `shape` of an array, in the SciPy sense:

* Reads and writes are bounds-checked against the shape
* This retains its value regardless of which values of a sparse array are or are not actually occupied
* Users can `resize`.
  * Some users need the ability to grow their datasets later, using either `tiledbsoma.io`'s append mode, or subsequent writes using the `tiledbsoma` API.
  * Note that the cellxgene census doesn't need this: eact week's published census has fixed shape, and any updates will happen in new storage, on a new week.

Using TileDB-SOMA up until the present:

* The TIleDB `domain` is immutable after array creation
  * This does bounds-checking for reads and writes, which is good
  * To leverage this to function as a `shape`, users would need to set the `domain` at array-creation time. However, users lose the ability to grow their datasets later.
* There is a `non_empty_domain` accessor
  * This only indicates min/max coordinates _at which data exists_. Consider an `X` array for 100 cells and 200 genes. If non-zero expression counts exist only for cell join IDs 2-17, then the `non_empty_domain` will indicate `(2,17)` along `soma_dim_0`.
  * Consider an `obms["X_pca"]` within the same experiment. This may be 100 cells by 50 PCA components: we need a placd to store the number 50.
  * Therefore users cannot leverage this to function as a `shape` accessor.
* We have offered a `used_shape` accessor since TileDB-SOMA 1.5.
  * This functions as a `shape` accessor, in the SciPy sense, but it is not multi-writer safe.

New feature for TileDB-SOMA 1.15:

* Arrays will have a  `shape`
* Reads and writes are bounds-checked against the shape
* This retains its value regardless of which values of a sparse array are or are not actually occupied
* Users can `resize`
* The `used_shape` accessor will be deprecated in TileDB-SOMA 1.13, and slated for removal in TileDB-SOMA 1.14.

Compatiblity:

This will now require users to do an explicit `resize` before appending/growing TileDB-SOMA Experiments. Guidance in the form of example notebooks will be provided.

##  Tracking

See also: [[sc-41074]](https://app.shortcut.com/tiledb-inc/story/41074) and [[sc-51048]](https://app.shortcut.com/tiledb-inc/story/51048).

## Scheduling

Support arrives in TileDB Core 2.25. Deprecations for TileDB-SOMA will be released with 1.13. Full support within TileDB-SOMA will be release in 1.14.

## Details

SOMA API mods as we've discussed in a Google doc are as follows.

### `SOMADataFrame`

* `create`: Retain the `domain` argument
  * Issue:
    * Core has a `(lo, hi)` tuple per dim, e.g. `(0,99)` or `(10,19)`
    * SOMA has count per dim, with 0 implicit: e.g. 100 or 20
    * For `SparseNDArray` and `DenseNDArray` core can have `(lo, hi)` and SOMA can have `count`
    * For `DataFrame` there can be multiple dims --- default is a single `soma_joinid`
    * That could be treated either in `(lo, hi)` fashion or `count` fashion
    * However additional dims (e.g. `cell_type`) can be on any type, including strings, floats, etc. where there is no implicit lo=0
    * Therefore we need to keep the current SOMA API wherein `DataFrame` takes a `domain` argument (in `(lo, hi)` fashion) and not a `shape` argument (in `count` fashion)

### `SparseNDArray and DenseNDArray`

* `create`
  * Have an optional shape argument which is of type `Tuple[Int,...]` where each element is the cell count of the corresponding dimension
    * If unsupplied, or if supplied but None in any slot: use the minimum 0 in each slot – nothing larger makes sense since we will not support downsize
  * User guidance should make clear that it will not be possible to create an ‘old’ style array with the ‘new style’ API. (See also the upgrade logic below.)

### All three of `SOMADataFrame`, `SparseNDArray`, `DenseNDArray`

* `write`
  * For new arrays, created with the new shape feature:
    * Core will bounds-check that coordinates provided at `write` time are within the current shape
    * Core will raise `tiledb.cc.TileDBError` to TileDB-SOMA, which will catch and raise `IndexError`, and R-standard behavior on the R side
  * For old arrays created before this feature:
    * Core will not bounds-check that coordinates provided at write time are within the current shape
* Existing `used_shape` accessor
  * TileDB-SOMA will deprecate this over a release cycle.
  * For new arrays: raise `NotImplementedError`
  * For old arrays: return what’s currently returned, with a deprecation warning.
  * Mechanism for determining old vs. new: `array.schema.version` (the core storage version).
* Existing `shape` accessor
  * For new arrays:
    * Have this return the new shape as proposed by core, no longer returning the TileDB domain.
  * For old arrays created before this feature:
    * Return the TileDB domain as now.
* Existing `non_empty_domain` accessor
  * Same behavior for old and new arrays (unaffected by this proposal).
  * Keep this accessor supported, but, with user notes that it’s generally non-useful
  * This should return None (or R equivalent) when there is a schema but no data have been written.
* New `maxshape` accessor
  * Maps the core-level `(lo, hi)` accessor for domain to count-style accessor hi+1. E.g. if the core domain is either `(0,99)` or `(50,99)` then TileDB-SOMA `maxshape` will say 100.
  * Same behavior for old and new arrays.
  * Let users query for what the TileDB domain is, with user notes that it’s the maximum that users can reshape to.
  * Issac suggests: maybe `domain` or `maxshape` (see h5py).
* New `resize` mutator
  * Note: `reshape` means something else in the community (numpy, zarr, h5py), e.g. a 5x20 (total 100 cells) being reinterpreted as 4x25 (still 100 cells). The standard name for changing cell-count is `resize`.
  * For old arrays created before this feature: raise `NotImplementedError`.
  * For new arrays:
    * Will raise `ValueError` if the new shape is smaller on any dim than currently in storage
    * Regardless of whether any data have been written whatsoever
    * Will raise `ValueError` if the new shape exceeds the TileDB domain from create time, which will serve TileDB-SOMA in a role of “max possible shape the user can reshape to”
    * Otherwise, any calls to write from this point will bounds-check writes within this new shape
    * **We don’t expect resize to be multi-writer safe with regard to write ; user notes must be clear on this point**
* New `tiledbsoma_upgrade_shape` method for SparseNDArray and DenseNDArray
  * This will leverage `array.schema.version` to see if an upgrade is needed
  * Leverage core support for storage-version updates
  * This will take a shape argument as in `create`
  * For arrays created with “just-right” size: this will succeed
  * For arrays created with “room-for-growth” / “two billion-ish” size: this will succeed
  * If the user passes a shape which exceeds the current TileDB domain: this will fail
* New `tiledbsoma_upgrade_domain method` for `DataFrame`
  * Same as for `SparseNDArray`/`DenseNDArray` except it will take a domain at the SOMA-API level just as `DataFrame`'s create method

### `tiledbsoma.io`

* The user-facing API has no shape arguments and thus won’t need changing.
* Internally to `tiledbsoma.io`, we’ll still ask the tiledbsoma API for the “big domain” (2 billionish)
* Append mode:
  * Will need a new `resize` method at the `Experiment` level
  * Users will need to:
    * Register as now
    * Call the experiment-level `resize`
      * Could be `exp.resize(...)`, or (better) this could be `tiledbsoma.io.reshape_experiment`
  * In either case: this method will take the new `obs` and `var` counts as inputs:
    * `exp.obs.reshape` to new `obs` count
    * `exp.ms[name].var.reshape` to new `var` count
    * `exp.ms[name].X[name].reshape` to new `obs` count x `var` count
    * `exp.ms[name].obsm[name].reshape` to new `obs` count x same width
    * `exp.ms[name].obsp[name].reshape` to new `obs` count x `obs` count
    * `exp.ms[name].varm[name].reshape` to new `var` count x same width
    * `exp.ms[name].varp[name].reshape` to new `var` count x `var` count
  * Do the individual append-mode writes as now



Discussion / hints:
#2785 is a quick-and-dirty concept-prover -- its sole function is to flush out any API misunderstandings we might have, in prep for 2.25.0 core release.

Fix patch:
diff --git a/libtiledbsoma/src/soma/soma_array.cc b/libtiledbsoma/src/soma/soma_array.cc
index 99138c94d1..b69e9caafd 100644
--- a/libtiledbsoma/src/soma/soma_array.cc
+++ b/libtiledbsoma/src/soma/soma_array.cc
@@ -1469,8 +1469,8 @@ std::pair<bool, std::string> SOMAArray::_can_set_shape_helper(
             return std::pair(
                 false,
                 fmt::format(
-                    "{}: array currently has no shape: please use "
-                    "tiledbsoma_upgrade_shape.",
+                    "{}: array currently has no shape: please "
+                    "upgrade the array.",
                     function_name_for_messages));
         }
     } else {
@@ -1480,8 +1480,7 @@ std::pair<bool, std::string> SOMAArray::_can_set_shape_helper(
             return std::pair(
                 false,
                 fmt::format(
-                    "{}: array already has a shape: please use resize rather "
-                    "than tiledbsoma_upgrade_shape.",
+                    "{}: array already has a shape: please use resize",
                     function_name_for_messages));
         }
     }
@@ -1723,23 +1722,152 @@ void SOMAArray::_set_soma_joinid_shape_helper(
     ArraySchema schema = arr_->schema();
     Domain domain = schema.domain();
     unsigned ndim = domain.ndim();
-
     auto tctx = ctx_->tiledb_ctx();
-    CurrentDomain old_current_domain = ArraySchemaExperimental::current_domain(
-        *tctx, schema);
-    NDRectangle ndrect = old_current_domain.ndrectangle();
-
-    CurrentDomain new_current_domain(*tctx);
     ArraySchemaEvolution schema_evolution(*tctx);
+    CurrentDomain new_current_domain(*tctx);
+
+    if (!is_resize) {
+        // For upgrade: copy from the full/wide/max domain except for the
+        // soma_joinid restriction.
+
+        NDRectangle ndrect(*tctx, domain);
+
+        for (unsigned i = 0; i < ndim; i++) {
+            const Dimension& dim = domain.dimension(i);
+            const std::string dim_name = dim.name();
+            if (dim_name == "soma_joinid") {
+                if (dim.type() != TILEDB_INT64) {
+                    throw TileDBSOMAError(fmt::format(
+                        "{}: expected soma_joinid to be of type {}; got {}",
+                        function_name_for_messages,
+                        tiledb::impl::type_to_str(TILEDB_INT64),
+                        tiledb::impl::type_to_str(dim.type())));
+                }
+                ndrect.set_range<int64_t>(dim_name, 0, newshape - 1);
+                continue;
 
-    for (unsigned i = 0; i < ndim; i++) {
-        if (domain.dimension(i).name() == "soma_joinid") {
-            ndrect.set_range<int64_t>(
-                domain.dimension(i).name(), 0, newshape - 1);
+                switch (dim.type()) {
+                    case TILEDB_STRING_ASCII:
+                    case TILEDB_STRING_UTF8:
+                    case TILEDB_CHAR:
+                        // TODO: make these named constants b/c they're shared
+                        // with arrow_adapter.
+                        ndrect.set_range(dim_name, "", "\xff");
+                        break;
+
+                    case TILEDB_INT8:
+                        ndrect.set_range<int8_t>(
+                            dim_name,
+                            dim.domain<int8_t>().first,
+                            dim.domain<int8_t>().second);
+                        break;
+                    case TILEDB_BOOL:
+                    case TILEDB_UINT8:
+                        ndrect.set_range<uint8_t>(
+                            dim_name,
+                            dim.domain<uint8_t>().first,
+                            dim.domain<uint8_t>().second);
+                        break;
+                    case TILEDB_INT16:
+                        ndrect.set_range<int16_t>(
+                            dim_name,
+                            dim.domain<int16_t>().first,
+                            dim.domain<int16_t>().second);
+                        break;
+                    case TILEDB_UINT16:
+                        ndrect.set_range<uint16_t>(
+                            dim_name,
+                            dim.domain<uint16_t>().first,
+                            dim.domain<uint16_t>().second);
+                        break;
+                    case TILEDB_INT32:
+                        ndrect.set_range<int32_t>(
+                            dim_name,
+                            dim.domain<int32_t>().first,
+                            dim.domain<int32_t>().second);
+                        break;
+                    case TILEDB_UINT32:
+                        ndrect.set_range<uint32_t>(
+                            dim_name,
+                            dim.domain<uint32_t>().first,
+                            dim.domain<uint32_t>().second);
+                        break;
+                    case TILEDB_INT64:
+                    case TILEDB_DATETIME_YEAR:
+                    case TILEDB_DATETIME_MONTH:
+                    case TILEDB_DATETIME_WEEK:
+                    case TILEDB_DATETIME_DAY:
+                    case TILEDB_DATETIME_HR:
+                    case TILEDB_DATETIME_MIN:
+                    case TILEDB_DATETIME_SEC:
+                    case TILEDB_DATETIME_MS:
+                    case TILEDB_DATETIME_US:
+                    case TILEDB_DATETIME_NS:
+                    case TILEDB_DATETIME_PS:
+                    case TILEDB_DATETIME_FS:
+                    case TILEDB_DATETIME_AS:
+                    case TILEDB_TIME_HR:
+                    case TILEDB_TIME_MIN:
+                    case TILEDB_TIME_SEC:
+                    case TILEDB_TIME_MS:
+                    case TILEDB_TIME_US:
+                    case TILEDB_TIME_NS:
+                    case TILEDB_TIME_PS:
+                    case TILEDB_TIME_FS:
+                    case TILEDB_TIME_AS:
+                        ndrect.set_range<int64_t>(
+                            dim_name,
+                            dim.domain<int64_t>().first,
+                            dim.domain<int64_t>().second);
+                        break;
+                    case TILEDB_UINT64:
+                        ndrect.set_range<uint64_t>(
+                            dim_name,
+                            dim.domain<int64_t>().first,
+                            dim.domain<int64_t>().second);
+                        break;
+                    case TILEDB_FLOAT32:
+                        ndrect.set_range<float>(
+                            dim_name,
+                            dim.domain<float>().first,
+                            dim.domain<float>().second);
+                        break;
+                    case TILEDB_FLOAT64:
+                        ndrect.set_range<double>(
+                            dim_name,
+                            dim.domain<double>().first,
+                            dim.domain<double>().second);
+                        break;
+                    default:
+                        throw TileDBSOMAError(fmt::format(
+                            "{}: internal error: unhandled type {} for {}.",
+                            function_name_for_messages,
+                            tiledb::impl::type_to_str(dim.type()),
+                            dim_name));
+                }
+            }
+        }
+
+        new_current_domain.set_ndrectangle(ndrect);
+
+    } else {
+        // For resize: copy from the existing current domain except for the
+        // new soma_joinid value.
+        CurrentDomain
+            old_current_domain = ArraySchemaExperimental::current_domain(
+                *tctx, schema);
+        NDRectangle ndrect = old_current_domain.ndrectangle();
+
+        for (unsigned i = 0; i < ndim; i++) {
+            if (domain.dimension(i).name() == "soma_joinid") {
+                ndrect.set_range<int64_t>(
+                    domain.dimension(i).name(), 0, newshape - 1);
+            }
         }
+
+        new_current_domain.set_ndrectangle(ndrect);
     }
 
-    new_current_domain.set_ndrectangle(ndrect);
     schema_evolution.expand_current_domain(new_current_domain);
     schema_evolution.array_evolve(uri_);
 }
@@ -1755,7 +1883,8 @@ std::vector<int64_t> SOMAArray::_tiledb_current_domain() {
 
     if (current_domain.is_empty()) {
         throw TileDBSOMAError(
-            "Internal error: current domain requested for an array which does "
+            "Internal error: current domain requested for an array which "
+            "does "
             "not support it");
     }
 
@@ -1868,7 +1997,8 @@ bool SOMAArray::_dims_are_int64() {
 void SOMAArray::_check_dims_are_int64() {
     if (!_dims_are_int64()) {
         throw TileDBSOMAError(
-            "[SOMAArray] internal coding error: expected all dims to be int64");
+            "[SOMAArray] internal coding error: expected all dims to be "
+            "int64");
     }
 }
 


Test patch:
diff --git a/libtiledbsoma/test/unit_soma_dataframe.cc b/libtiledbsoma/test/unit_soma_dataframe.cc
index 942e0f8f28..eb9fa04a2a 100644
--- a/libtiledbsoma/test/unit_soma_dataframe.cc
+++ b/libtiledbsoma/test/unit_soma_dataframe.cc
@@ -563,12 +563,12 @@ TEST_CASE_METHOD(
 
         REQUIRE(ned_sjid == std::vector<int64_t>({1, 2}));
 
-        REQUIRE(dom_sjid == std::vector<int64_t>({0, 99}));
+        REQUIRE(dom_sjid == std::vector<int64_t>({0, SOMA_JOINID_DIM_MAX}));
 
         REQUIRE(maxdom_sjid.size() == 2);
         REQUIRE(maxdom_sjid[0] == 0);
         if (!use_current_domain) {
-            REQUIRE(maxdom_sjid[1] == 99);
+            REQUIRE(maxdom_sjid[1] == SOMA_JOINID_DIM_MAX);
         } else {
             REQUIRE(maxdom_sjid[1] > 2000000000);
         }
@@ -662,11 +662,14 @@ TEST_CASE_METHOD(
 
         if (!use_current_domain) {
             REQUIRE(ned_sjid == std::vector<int64_t>({1, 10}));
-            REQUIRE(dom_sjid == std::vector<int64_t>({0, 99}));
-            REQUIRE(maxdom_sjid == std::vector<int64_t>({0, 99}));
+            REQUIRE(dom_sjid == std::vector<int64_t>({0, SOMA_JOINID_DIM_MAX}));
+            REQUIRE(
+                maxdom_sjid == std::vector<int64_t>({0, SOMA_JOINID_DIM_MAX}));
         } else {
             REQUIRE(ned_sjid == std::vector<int64_t>({1, 101}));
-            REQUIRE(dom_sjid == std::vector<int64_t>({0, 199}));
+            REQUIRE(
+                dom_sjid ==
+                std::vector<int64_t>({0, SOMA_JOINID_RESIZE_DIM_MAX}));
             REQUIRE(maxdom_sjid.size() == 2);
             REQUIRE(maxdom_sjid[0] == 0);
             REQUIRE(maxdom_sjid[1] > 2000000000);
@@ -680,6 +683,21 @@ TEST_CASE_METHOD(
             REQUIRE(
                 check.second ==
                 "testing: dataframe currently has no domain set.");
+
+            REQUIRE(!sdf->has_current_domain());
+            sdf->close();
+
+            sdf = open(OpenMode::write);
+            sdf->upgrade_soma_joinid_shape(SOMA_JOINID_DIM_MAX + 1, "testing");
+            sdf->close();
+
+            sdf = open(OpenMode::read);
+            REQUIRE(sdf->has_current_domain());
+            std::optional<int64_t> actual = sdf->maybe_soma_joinid_shape();
+            REQUIRE(actual.has_value());
+            REQUIRE(actual.value() == SOMA_JOINID_DIM_MAX + 1);
+            sdf->close();
+
         } else {
             // Must fail since this is too small.
             REQUIRE(check.first == false);