unit-test coverage

apis/python/src/tiledbsoma/_dataframe.py

@@ -6,7 +6,18 @@
 """
 Implementation of a SOMA DataFrame
 """
-from typing import Any, List, Optional, Sequence, Tuple, Type, Union, cast
+from typing import (
+    Any,
+    Dict,
+    Iterable,
+    List,
+    Optional,
+    Sequence,
+    Tuple,
+    Type,
+    Union,
+    cast,
+)
 
 import numpy as np
 import pyarrow as pa
@@ -485,6 +496,11 @@ def _upgrade_or_change_domain_helper(
                 f"{function_name_for_messages}: requested domain has length {len(dim_names)} but the dataframe's schema has index-column count {len(newdomain)}"
             )
 
+        if any([len(slot) != 2 for slot in newdomain]):  # type: ignore
+            raise ValueError(
+                f"{function_name_for_messages}: requested domain must have low,high pairs in each slot"
+            )
+
         # From the dataframe's schema, extract the subschema for only index columns (TileDB dimensions).
         full_schema = self.schema
         dim_schema_list = []
@@ -493,9 +509,22 @@ def _upgrade_or_change_domain_helper(
         dim_schema = pa.schema(dim_schema_list)
 
         # Convert the user's tuple of low/high pairs into a dict keyed by index-column name.
-        new_domain_dict = {}
+        new_domain_dict: Dict[str, Iterable[Any]] = {}
         for i, dim_name in enumerate(dim_names):
-            new_domain_dict[dim_name] = newdomain[i]
+            # Domain can't be specified for strings (core constraint) so let them keystroke that easily.
+            if (
+                dim_schema.field(dim_name).type
+                in [
+                    pa.string(),
+                    pa.large_string(),
+                    pa.binary(),
+                    pa.large_binary(),
+                ]
+                and newdomain[i] is None
+            ):
+                new_domain_dict[dim_name] = ("", "")
+            else:
+                new_domain_dict[dim_name] = tuple(newdomain[i])  # type: ignore
 
         # Return this as a pyarrow table. This has n columns where n is the number of
         # index columns, and two rows: one row for the low values and one for the high values.

apis/python/tests/test_shape.py

@@ -356,6 +356,103 @@ def test_dataframe_basics(tmp_path, soma_joinid_domain, index_column_names):
             sdf.write(data)
 
 
+def test_domain_mods(tmp_path):
+    if not tiledbsoma._flags.NEW_SHAPE_FEATURE_FLAG_ENABLED:
+        return
+
+    uri = tmp_path.as_posix()
+
+    schema = pa.schema(
+        [
+            ("soma_joinid", pa.int64()),
+            ("mystring", pa.string()),
+            ("myint", pa.int16()),
+            ("myfloat", pa.float32()),
+            ("mybool", pa.bool_()),  # not supported as an index type
+        ]
+    )
+    index_column_names = ["soma_joinid", "mystring", "myint", "myfloat"]
+
+    domain_for_create = [
+        [0, 3],
+        None,
+        [20, 50],
+        [0.0, 6.0],
+    ]
+
+    data_dict = {
+        "soma_joinid": [0, 1, 2, 3],
+        "mystring": ["a", "b", "a", "b"],
+        "myint": [20, 30, 40, 50],
+        "myfloat": [1.0, 2.5, 4.0, 5.5],
+        "mybool": [True, False, True, True],
+    }
+
+    data = pa.Table.from_pydict(data_dict)
+
+    with tiledbsoma.DataFrame.create(
+        uri,
+        schema=schema,
+        index_column_names=index_column_names,
+        domain=domain_for_create,
+    ) as sdf:
+        sdf.write(data)
+
+    # Check "expand" to same
+    with tiledbsoma.DataFrame.open(uri, "w") as sdf:
+        newdomain = [[0, 3], None, [20, 50], [0.0, 6.0]]
+        ok, msg = sdf.change_domain(newdomain, check_only=True)
+        assert ok
+        assert msg == ""
+
+    # Shrink
+    with tiledbsoma.DataFrame.open(uri, "w") as sdf:
+        newdomain = [[0, 2], None, [20, 50], [0.0, 6.0]]
+        ok, msg = sdf.change_domain(newdomain, check_only=True)
+        assert not ok
+        assert "downsize is unsupported" in msg
+
+    with tiledbsoma.DataFrame.open(uri, "w") as sdf:
+        newdomain = [[0, 3], None, [20, 40], [0.0, 6.0]]
+        ok, msg = sdf.change_domain(newdomain, check_only=True)
+        assert not ok
+        assert "downsize is unsupported" in msg
+
+    with tiledbsoma.DataFrame.open(uri, "w") as sdf:
+        newdomain = [[0, 3], None, [20, 50], [1.0, 6.0]]
+        ok, msg = sdf.change_domain(newdomain, check_only=True)
+        assert not ok
+        assert "downsize is unsupported" in msg
+
+    # String domain cannot be specified
+    with tiledbsoma.DataFrame.open(uri, "w") as sdf:
+        newdomain = [
+            [0, 3],
+            ["a", "z"],
+            [20, 50],
+            [0.0, 6.0],
+        ]
+        ok, msg = sdf.change_domain(newdomain, check_only=True)
+        assert not ok
+        assert "domain cannot be set for string index columns" in msg
+
+    # All clear
+    with tiledbsoma.DataFrame.open(uri, "w") as sdf:
+        newdomain = [[0, 9], None, [0, 100], [-10.0, 10.0]]
+        ok, msg = sdf.change_domain(newdomain, check_only=True)
+        assert ok
+        assert msg == ""
+        sdf.change_domain(newdomain)
+
+    # Check for success
+    with tiledbsoma.DataFrame.open(uri, "r") as sdf:
+        dom = sdf.domain
+        assert dom[0] == (0, 9)
+        assert dom[1] == ("", "")
+        assert dom[2] == (0, 100)
+        assert dom[3] == (-10.0, 10.0)
+
+
 @pytest.mark.parametrize("has_shapes", [False, True])
 def test_canned_experiments(tmp_path, has_shapes):
     uri = tmp_path.as_posix()
@@ -435,6 +532,28 @@ def _check_ndarray(ndarray, has_shapes, expected_shape):
     assert "[SparseNDArray] ms/RNA/obsp/distances" in body
     assert "ms/RNA/obsm/X_draw_graph_fr" in body
 
+    # Check upgrade_domain for dataframes
+    with tiledbsoma.Experiment.open(uri, "w") as exp:
+
+        ok, msg = exp.obs.tiledbsoma_upgrade_domain([[10, 4]], check_only=True)
+        if has_shapes:
+            assert not ok
+            assert "dataframe already has a domain" in msg
+        else:
+            assert not ok
+            assert "new lower > new upper" in msg
+
+        ok, msg = exp.obs.tiledbsoma_upgrade_domain([[0, 1]], check_only=True)
+        if has_shapes:
+            assert not ok
+            assert "dataframe already has a domain" in msg
+        else:
+            assert ok
+            assert msg == ""
+
+        with pytest.raises(ValueError):
+            exp.obs.tiledbsoma_upgrade_domain([[0, 1, 2]], check_only=True)
+
     # Check dry run of tiledbsoma.io.upgrade_experiment_shapes
     handle = io.StringIO()
     upgradeable = tiledbsoma.io.upgrade_experiment_shapes(