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 fbcd1695f2..e59c5bc8b3 100644
--- a/libtiledbsoma/src/soma/soma_array.cc
+++ b/libtiledbsoma/src/soma/soma_array.cc
@@ -1012,6 +1012,16 @@ std::vector<std::string> SOMAArray::dimension_names() const {
     return result;
 }
 
+bool SOMAArray::has_dimension_name(const std::string& name) const {
+    auto dimensions = tiledb_schema()->domain().dimensions();
+    for (const auto& dim : dimensions) {
+        if (dim.name() == name) {
+            return true;
+        }
+    }
+    return false;
+}
+
 void SOMAArray::write(bool sort_coords) {
     if (mq_->query_type() != TILEDB_WRITE) {
         throw TileDBSOMAError("[SOMAArray] array must be opened in write mode");
@@ -1418,6 +1428,192 @@ std::vector<int64_t> SOMAArray::maxshape() {
     return _tiledb_domain();
 }
 
+// This is a helper for can_upgrade_domain and can_resize, which have
+// much overlap.
+std::pair<bool, std::string> SOMAArray::_can_set_shape_helper(
+    const std::vector<int64_t>& newshape,
+    bool is_resize,
+    std::string method_name_for_messages) {
+    // E.g. it's an error to try to upgrade_domain or resize specifying
+    // a 3-D shape on a 2-D array.
+    auto arg_ndim = newshape.size();
+    auto array_ndim = arr_->schema().domain().ndim();
+    if (array_ndim != arg_ndim) {
+        return std::pair(
+            false,
+            fmt::format(
+                "cannot {}: provided shape has ndim {}, while the array has {}",
+                method_name_for_messages,
+                arg_ndim,
+                array_ndim));
+    }
+
+    // Enforce the semantics that tiledbsoma_upgrade_domain must be called
+    // only on arrays that don't have a shape set, and resize must be called
+    // only on arrays that do.
+    bool has_shape = has_current_domain();
+    if (is_resize) {
+        // They're trying to do resize on an array that doesn't already have a
+        // shape.
+        if (!has_shape) {
+            return std::pair(
+                false,
+                fmt::format(
+                    "{}: array currently has no shape: please use "
+                    "tiledbsoma_upgrade_shape.",
+                    method_name_for_messages));
+        }
+    } else {
+        // They're trying to do upgrade_shape on an array that already has a
+        // shape.
+        if (has_shape) {
+            return std::pair(
+                false,
+                fmt::format(
+                    "{}: array already has a shape: please use resize rather "
+                    "than "
+                    "tiledbsoma_upgrade_shape.",
+                    method_name_for_messages));
+        }
+    }
+
+    // * For old-style arrays without shape: core domain (soma maxdomain) may be
+    //   small (like 100) or big (like 2 billionish).
+    // * For new-style arrays with shape: core current domain (soma domain) will
+    //   probably be small and core domain (soma maxdomain) will be huge.
+    //
+    // In either case, we need to check that the user's requested shape isn't
+    // outside the core domain, which is immutable. For old-style arrays,
+    //
+    // if the requested shape fits in the array's core domain, it's good to go
+    // as a new shape.
+    auto domain_check = _can_set_shape_domainish_helper(
+        newshape, false, method_name_for_messages);
+    if (!domain_check.first) {
+        return domain_check;
+    }
+
+    // For new-style arrays, we need to additionally that the the requested
+    // shape (core current domain) isn't a downsize of the current one.
+    if (has_shape) {
+        auto current_domain_check = _can_set_shape_domainish_helper(
+            newshape, true, method_name_for_messages);
+        if (!current_domain_check.first) {
+            return current_domain_check;
+        }
+    }
+
+    return std::pair(true, "");
+}
+
+// This is a helper for _can_set_shape_helper: it's used for comparing
+// the user's requested shape against the core current domain or core (max)
+// domain.
+std::pair<bool, std::string> SOMAArray::_can_set_shape_domainish_helper(
+    const std::vector<int64_t>& newshape,
+    bool check_current_domain,
+    std::string method_name_for_messages) {
+    Domain domain = arr_->schema().domain();
+
+    for (unsigned i = 0; i < domain.ndim(); i++) {
+        const auto& dim = domain.dimension(i);
+
+        const std::string& dim_name = dim.name();
+
+        // These methods are only for SOMA NDArrays, and any other arrays for
+        // which the indices are entirely int64.  SOMA DataFrame objects, with
+        // multi-type dims, need to go through upgrade_domain -- and this is
+        // library-internal code, it's not the user's fault if we got here.
+        if (dim.type() != TILEDB_INT64) {
+            throw TileDBSOMAError(fmt::format(
+                "{}: internal error: expected {} dim to "
+                "be {}; got {}",
+                method_name_for_messages,
+                dim_name,
+                tiledb::impl::type_to_str(TILEDB_INT64),
+                tiledb::impl::type_to_str(dim.type())));
+        }
+
+        if (check_current_domain) {
+            std::pair<int64_t, int64_t>
+                cap = _core_current_domain_slot<int64_t>(dim_name);
+            int64_t old_dim_shape = cap.second + 1;
+
+            if (newshape[i] < old_dim_shape) {
+                return std::pair(
+                    false,
+                    fmt::format(
+                        "cannot {} for {}: new {} < existing shape {}",
+                        method_name_for_messages,
+                        dim_name,
+                        newshape[i],
+                        old_dim_shape));
+            }
+
+        } else {
+            std::pair<int64_t, int64_t> cap = _core_domain_slot<int64_t>(
+                dim_name);
+            int64_t old_dim_shape = cap.second + 1;
+
+            if (newshape[i] > old_dim_shape) {
+                return std::pair(
+                    false,
+                    fmt::format(
+                        "cannot {} for {}: new {} < maxshape {}",
+                        method_name_for_messages,
+                        dim_name,
+                        newshape[i],
+                        old_dim_shape));
+            }
+        }
+    }
+    return std::pair(true, "");
+}
+
+std::pair<bool, std::string> SOMAArray::can_resize_soma_joinid(
+    int64_t newshape) {
+    // Fail if the array doesn't already have a shape yet (they should upgrade
+    // first).
+    if (!has_current_domain()) {
+        return std::pair(
+            false,
+            "can_resize_soma_joinid: dataframe currently has no domain set: "
+            "please use tiledbsoma_upgrade_domain.");
+    }
+
+    // OK if soma_joinid isn't a dim.
+    if (!has_dimension_name("soma_joinid")) {
+        return std::pair(true, "");
+    }
+
+    // Fail if the newshape isn't within the array's core current domain.
+    std::pair cur_dom_lo_hi = _core_current_domain_slot<int64_t>("soma_joinid");
+    if (newshape < cur_dom_lo_hi.second) {
+        return std::pair(
+            false,
+            fmt::format(
+                "cannot resize_soma_joinid: new soma_joinid shape {} < "
+                "existing shape {}",
+                newshape,
+                cur_dom_lo_hi.second));
+    }
+
+    // Fail if the newshape isn't within the array's core (max) domain.
+    std::pair dom_lo_hi = _core_domain_slot<int64_t>("soma_joinid");
+    if (newshape > dom_lo_hi.second) {
+        return std::pair(
+            false,
+            fmt::format(
+                "cannot resize_soma_joinid: new soma_joinid shape {} > "
+                "maxshape {}",
+                newshape,
+                dom_lo_hi.second));
+    }
+
+    // Sucess otherwise.
+    return std::pair(true, "");
+}
+
 void SOMAArray::resize(const std::vector<int64_t>& newshape) {
     if (_get_current_domain().is_empty()) {
         throw TileDBSOMAError(
diff --git a/libtiledbsoma/src/soma/soma_array.h b/libtiledbsoma/src/soma/soma_array.h
index 67903bbeb6..43c17b18e4 100644
--- a/libtiledbsoma/src/soma/soma_array.h
+++ b/libtiledbsoma/src/soma/soma_array.h
@@ -290,6 +290,13 @@ class SOMAArray : public SOMAObject {
      */
     std::vector<std::string> dimension_names() const;
 
+    /**
+     * @brief Sees if the array has a dimension of the given name.
+     *
+     * @return bool
+     */
+    bool has_dimension_name(const std::string& name) const;
+
     /**
      * @brief Set the dimension slice using one point
      *
@@ -1031,6 +1038,55 @@ class SOMAArray : public SOMAObject {
      */
     std::vector<int64_t> maxshape();
 
+    /**
+     * This wires up to Python/R to tell a user if they can call resize() on an
+     * array without error. For single arrays, they could just call resize() and
+     * take their chances -- but for experiment-level resize (e.g. append mode)
+     * it's crucial that we provide a can-we-do-them-all pass through all arrays
+     * in the experiment before attempting any of them.
+     *
+     * On failure, returns false and an error string suitable for showing
+     * to the user; on success, returns true and the empty string.
+     *
+     * Failure reasons: the requested shape's dimension-count doesn't match the
+     * arrays; the array doesn't have a shape set (they must call
+     * upgrade_shape), or the requested shape doesn't fit within the array's
+     * existing core domain.
+     */
+    std::pair<bool, std::string> can_resize(
+        const std::vector<int64_t>& newshape) {
+        return _can_set_shape_helper(newshape, true, "resize");
+    }
+
+    /**
+     * This wires up to Python/R to tell a user if they can call
+     * upgrade_shape() on an array without error. For single dataframes,
+     * they could just call upgrade_shape() and take their chances -- but for
+     * experiment-level resize (e.g. append mode) it's crucial that we provide a
+     * can-we-do-them-all pass through all arrays in the experiment before
+     * attempting any of them.
+     *
+     * On failure, returns false and an error string suitable for showing
+     * to the user; on success, returns true and the empty string.
+     *
+     * Failure reasons: the requested shape's dimension-count doesn't match the
+     * arrays; the array already has a shape set (they must call resize), the
+     * requested shape doesn't fit within the array's existing core domain, or
+     * the requested shape is a downsize of the array's existing core current
+     * domain.
+     */
+    std::pair<bool, std::string> can_upgrade_shape(
+        const std::vector<int64_t>& newshape) {
+        return _can_set_shape_helper(
+            newshape, false, "tiledbsoma_upgrade_shape");
+    }
+
+    /**
+     * This is similar to can_upgrade_shape, but it's a can-we call
+     * for maybe_resize_soma_joinid.
+     */
+    std::pair<bool, std::string> can_resize_soma_joinid(int64_t newshape);
+
     /**
      * @brief Resize the shape (what core calls "current domain") up to the
      * maxshape (what core calls "domain").
@@ -1125,7 +1181,23 @@ class SOMAArray : public SOMAObject {
     }
 
     /**
-     * Helper method for resize and upgrade_shape.
+     * This is a code-dedupe helper for can_resize and can_upgrade_domain.
+     */
+    std::pair<bool, std::string> _can_set_shape_helper(
+        const std::vector<int64_t>& newshape,
+        bool is_resize,
+        std::string method_name_for_messages);
+
+    /**
+     * This is a second-level code-dedupe helper for _can_set_shape_helper.
+     */
+    std::pair<bool, std::string> _can_set_shape_domainish_helper(
+        const std::vector<int64_t>& newshape,
+        bool check_current_domain,
+        std::string method_name_for_messages);
+
+    /**
+     * This is a code-dedupe helper method for resize and upgrade_shape.
      */
     void _set_current_domain_from_shape(const std::vector<int64_t>& newshape);
 


Test patch:
diff --git a/libtiledbsoma/test/unit_soma_dataframe.cc b/libtiledbsoma/test/unit_soma_dataframe.cc
index ae20d2eda3..eb298e51be 100644
--- a/libtiledbsoma/test/unit_soma_dataframe.cc
+++ b/libtiledbsoma/test/unit_soma_dataframe.cc
@@ -664,6 +664,28 @@ TEST_CASE_METHOD(
             REQUIRE(maxdom_sjid[1] > 2000000000);
         }
 
+        // Check can_resize_soma_joinid
+        std::pair<bool, std::string> check = soma_dataframe
+                                                 ->can_resize_soma_joinid(1);
+        if (!use_current_domain) {
+            REQUIRE(check.first == false);
+            REQUIRE(
+                check.second ==
+                "can_resize_soma_joinid: dataframe currently has no domain "
+                "set: please use tiledbsoma_upgrade_domain.");
+        } else {
+            // Must fail since this is too small.
+            REQUIRE(check.first == false);
+            REQUIRE(
+                check.second ==
+                "cannot resize_soma_joinid: new soma_joinid shape 1 < existing "
+                "shape 199");
+            check = soma_dataframe->can_resize_soma_joinid(
+                SOMA_JOINID_RESIZE_DIM_MAX + 1);
+            REQUIRE(check.first == true);
+            REQUIRE(check.second == "");
+        }
+
         soma_dataframe->close();
     }
 }
@@ -878,6 +900,28 @@ TEST_CASE_METHOD(
             REQUIRE(maxdom_u32[1] > 2000000000);
         }
 
+        // Check can_resize_soma_joinid
+        std::pair<bool, std::string> check = soma_dataframe
+                                                 ->can_resize_soma_joinid(1);
+        if (!use_current_domain) {
+            REQUIRE(check.first == false);
+            REQUIRE(
+                check.second ==
+                "can_resize_soma_joinid: dataframe currently has no domain "
+                "set: please use tiledbsoma_upgrade_domain.");
+        } else {
+            // Must fail since this is too small.
+            REQUIRE(check.first == false);
+            REQUIRE(
+                check.second ==
+                "cannot resize_soma_joinid: new soma_joinid shape 1 < existing "
+                "shape 199");
+            check = soma_dataframe->can_resize_soma_joinid(
+                SOMA_JOINID_RESIZE_DIM_MAX + 1);
+            REQUIRE(check.first == true);
+            REQUIRE(check.second == "");
+        }
+
         soma_dataframe->close();
     }
 }
@@ -1108,6 +1152,28 @@ TEST_CASE_METHOD(
 
         REQUIRE(ned_str == std::vector<std::string>({"", ""}));
 
+        // Check can_resize_soma_joinid
+        std::pair<bool, std::string> check = soma_dataframe
+                                                 ->can_resize_soma_joinid(1);
+        if (!use_current_domain) {
+            REQUIRE(check.first == false);
+            REQUIRE(
+                check.second ==
+                "can_resize_soma_joinid: dataframe currently has no domain "
+                "set: please use tiledbsoma_upgrade_domain.");
+        } else {
+            // Must fail since this is too small.
+            REQUIRE(check.first == false);
+            REQUIRE(
+                check.second ==
+                "cannot resize_soma_joinid: new soma_joinid shape 1 < existing "
+                "shape 99");
+            check = soma_dataframe->can_resize_soma_joinid(
+                SOMA_JOINID_RESIZE_DIM_MAX + 1);
+            REQUIRE(check.first == true);
+            REQUIRE(check.second == "");
+        }
+
         soma_dataframe->close();
     }
 }
@@ -1299,6 +1365,21 @@ TEST_CASE_METHOD(
             REQUIRE(maxdom_str == std::vector<std::string>({"", ""}));
         }
 
+        // Check can_resize_soma_joinid
+        std::pair<bool, std::string> check = soma_dataframe
+                                                 ->can_resize_soma_joinid(0);
+        if (!use_current_domain) {
+            REQUIRE(check.first == false);
+            REQUIRE(
+                check.second ==
+                "can_resize_soma_joinid: dataframe currently has no domain "
+                "set: please use tiledbsoma_upgrade_domain.");
+        } else {
+            // Must pass since soma_joinid isn't a dim in this case.
+            REQUIRE(check.first == true);
+            REQUIRE(check.second == "");
+        }
+
         soma_dataframe->close();
     }
 }
diff --git a/libtiledbsoma/test/unit_soma_sparse_ndarray.cc b/libtiledbsoma/test/unit_soma_sparse_ndarray.cc
index bb6b2decc4..9315a8724b 100644
--- a/libtiledbsoma/test/unit_soma_sparse_ndarray.cc
+++ b/libtiledbsoma/test/unit_soma_sparse_ndarray.cc
@@ -340,3 +340,141 @@ TEST_CASE("SOMASparseNDArray: metadata", "[SOMASparseNDArray]") {
         REQUIRE(soma_sparse->metadata_num() == 2);
     }
 }
+void breakme() {
+}
+
+TEST_CASE(
+    "SOMASparseNDArray: can_tiledbsoma_upgrade_shape", "[SOMASparseNDArray]") {
+    int64_t dim_max = 999;
+
+    auto ctx = std::make_shared<SOMAContext>();
+    std::string uri = "mem://unit-test-sparse-ndarray-upgrade-shape";
+
+    std::string dim_name = "soma_dim_0";
+    tiledb_datatype_t dim_tiledb_datatype = TILEDB_INT64;
+    tiledb_datatype_t attr_tiledb_datatype = TILEDB_INT32;
+    std::string dim_arrow_format = ArrowAdapter::tdb_to_arrow_type(
+        dim_tiledb_datatype);
+    std::string attr_arrow_format = ArrowAdapter::tdb_to_arrow_type(
+        attr_tiledb_datatype);
+
+    std::vector<helper::DimInfo> dim_infos(
+        {{.name = dim_name,
+          .tiledb_datatype = dim_tiledb_datatype,
+          .dim_max = dim_max,
+          .string_lo = "N/A",
+          .string_hi = "N/A",
+          .use_current_domain = false}});
+
+    auto index_columns = helper::create_column_index_info(dim_infos);
+
+    SOMASparseNDArray::create(
+        uri,
+        attr_arrow_format,
+        ArrowTable(
+            std::move(index_columns.first), std::move(index_columns.second)),
+        ctx);
+
+    auto soma_sparse = SOMASparseNDArray::open(uri, OpenMode::write, ctx);
+    REQUIRE(soma_sparse->has_current_domain() == false);
+
+    // For old-style arrays, from before the current-domain feature:
+    // * The shape specified at create becomes the core (max) domain
+    //   o Recall that the core domain is immutable
+    // * There is no current domain set
+    //   o A current domain can be applied to it, up to <= (max) domain
+    auto dom = soma_sparse->soma_domain_slot<int64_t>(dim_name);
+    auto mxd = soma_sparse->soma_maxdomain_slot<int64_t>(dim_name);
+    REQUIRE(dom == mxd);
+    REQUIRE(dom.first == 0);
+    REQUIRE(dom.second == dim_max);
+
+    breakme();
+    std::vector<int64_t> newshape_wrong_dims({dim_max, 12});
+    std::vector<int64_t> newshape_too_big({dim_max + 10});
+    std::vector<int64_t> newshape_good({40});
+
+    auto check = soma_sparse->can_upgrade_shape(newshape_wrong_dims);
+    REQUIRE(check.first == false);
+    REQUIRE(
+        check.second ==
+        "cannot tiledbsoma_upgrade_shape: provided shape has ndim 2, while the "
+        "array has 1");
+
+    check = soma_sparse->can_upgrade_shape(newshape_too_big);
+    REQUIRE(check.first == false);
+    REQUIRE(
+        check.second ==
+        "cannot tiledbsoma_upgrade_shape for soma_dim_0: new 1009 < maxshape "
+        "1000");
+
+    check = soma_sparse->can_upgrade_shape(newshape_good);
+    REQUIRE(check.first == true);
+    REQUIRE(check.second == "");
+}
+
+TEST_CASE("SOMASparseNDArray: can_resize", "[SOMASparseNDArray]") {
+    int64_t dim_max = 999;
+
+    auto ctx = std::make_shared<SOMAContext>();
+    std::string uri = "mem://unit-test-sparse-ndarray-resize";
+
+    std::string dim_name = "soma_dim_0";
+    tiledb_datatype_t dim_tiledb_datatype = TILEDB_INT64;
+    tiledb_datatype_t attr_tiledb_datatype = TILEDB_INT32;
+    std::string dim_arrow_format = ArrowAdapter::tdb_to_arrow_type(
+        dim_tiledb_datatype);
+    std::string attr_arrow_format = ArrowAdapter::tdb_to_arrow_type(
+        attr_tiledb_datatype);
+
+    std::vector<helper::DimInfo> dim_infos(
+        {{.name = dim_name,
+          .tiledb_datatype = dim_tiledb_datatype,
+          .dim_max = dim_max,
+          .string_lo = "N/A",
+          .string_hi = "N/A",
+          .use_current_domain = true}});
+
+    auto index_columns = helper::create_column_index_info(dim_infos);
+
+    SOMASparseNDArray::create(
+        uri,
+        attr_arrow_format,
+        ArrowTable(
+            std::move(index_columns.first), std::move(index_columns.second)),
+        ctx);
+
+    auto soma_sparse = SOMASparseNDArray::open(uri, OpenMode::write, ctx);
+    REQUIRE(soma_sparse->has_current_domain() == true);
+
+    // For new-style arrays, with the current-domain feature:
+    // * The shape specified at create becomes the core current domain
+    //   o Recall that the core current domain is mutable, up tp <= (max) domain
+    // * The core (max) domain is huge
+    //   o Recall that the core max domain is immutable
+    auto dom = soma_sparse->soma_domain_slot<int64_t>(dim_name);
+    auto mxd = soma_sparse->soma_maxdomain_slot<int64_t>(dim_name);
+    REQUIRE(dom != mxd);
+    REQUIRE(dom.first == 0);
+    REQUIRE(dom.second == dim_max);
+
+    std::vector<int64_t> newshape_wrong_dims({dim_max, 12});
+    std::vector<int64_t> newshape_too_small({40});
+    std::vector<int64_t> newshape_good({2000});
+
+    auto check = soma_sparse->can_resize(newshape_wrong_dims);
+    REQUIRE(check.first == false);
+    REQUIRE(
+        check.second ==
+        "cannot resize: provided shape has ndim 2, while the array has 1");
+
+    check = soma_sparse->can_resize(newshape_too_small);
+    REQUIRE(check.first == false);
+    REQUIRE(
+        check.second ==
+        "cannot resize for soma_dim_0: new 40 < existing shape 1000");
+
+    check = soma_sparse->can_resize(newshape_good);
+    REQUIRE(check.first == true);
+    REQUIRE(check.second == "");
+}