Fix bug with join with duplicate obs indices

src/spatialdata/_core/query/relational_query.py

@@ -380,7 +380,8 @@ def _inner_join_spatialelement_table(
     element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
 ) -> tuple[dict[str, Any], AnnData]:
     regions, region_column_name, instance_key = get_table_keys(table)
-    groups_df = table.obs.groupby(by=region_column_name, observed=False)
+    obs = table.obs.reset_index()
+    groups_df = obs.groupby(by=region_column_name, observed=False)
     joined_indices = None
     for element_type, name_element in element_dict.items():
         for name, element in name_element.items():
@@ -401,7 +402,7 @@ def _inner_join_spatialelement_table(
                 element_dict[element_type][name] = masked_element
 
                 joined_indices = _get_joined_table_indices(
-                    joined_indices, element_indices, table_instance_key_column, match_rows
+                    joined_indices, masked_element.index, table_instance_key_column, match_rows
                 )
             else:
                 warnings.warn(
@@ -414,6 +415,7 @@ def _inner_join_spatialelement_table(
         joined_indices = joined_indices.dropna() if any(joined_indices.isna()) else joined_indices
 
     joined_table = table[joined_indices, :].copy() if joined_indices is not None else None
+
     _inplace_fix_subset_categorical_obs(subset_adata=joined_table, original_adata=table)
     return element_dict, joined_table
 
@@ -455,7 +457,8 @@ def _left_join_spatialelement_table(
     if match_rows == "right":
         warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
     regions, region_column_name, instance_key = get_table_keys(table)
-    groups_df = table.obs.groupby(by=region_column_name, observed=False)
+    obs = table.obs.reset_index()
+    groups_df = obs.groupby(by=region_column_name, observed=False)
     joined_indices = None
     for element_type, name_element in element_dict.items():
         for name, element in name_element.items():

tests/core/query/test_relational_query.py

@@ -3,14 +3,15 @@
 import pytest
 from anndata import AnnData
 
-from spatialdata import get_values, match_table_to_element
+from spatialdata import SpatialData, get_values, match_table_to_element
 from spatialdata._core.query.relational_query import (
     _locate_value,
     _ValueOrigin,
     get_element_annotators,
     join_spatialelement_table,
 )
 from spatialdata.models.models import TableModel
+from spatialdata.testing import assert_anndata_equal, assert_geodataframe_equal
 
 
 def test_match_table_to_element(sdata_query_aggregation):
@@ -376,6 +377,47 @@ def test_match_rows_inner_join_non_matching_table(sdata_query_aggregation):
     assert all(indices == reversed_instance_id)
 
 
+# TODO: 'left_exclusive' is currently not working, reported in this issue:
+@pytest.mark.parametrize("join_type", ["left", "right", "inner", "right_exclusive"])
+def test_inner_join_match_rows_duplicate_obs_indices(sdata_query_aggregation: SpatialData, join_type: str) -> None:
+    sdata = sdata_query_aggregation
+    sdata["table"].obs.index = ["a"] * sdata["table"].n_obs
+    sdata["values_circles"] = sdata_query_aggregation["values_circles"][:4]
+    sdata["values_polygons"] = sdata_query_aggregation["values_polygons"][:5]
+
+    element_dict, table = join_spatialelement_table(
+        sdata=sdata,
+        spatial_element_names=["values_circles", "values_polygons"],
+        table_name="table",
+        how=join_type,
+    )
+
+    if join_type in ["left", "inner"]:
+        # table check
+        assert table.n_obs == 9
+        assert np.array_equal(table.obs["instance_id"][:4], sdata["values_circles"].index)
+        assert np.array_equal(table.obs["instance_id"][4:], sdata["values_polygons"].index)
+        # shapes check
+        assert_geodataframe_equal(element_dict["values_circles"], sdata["values_circles"])
+        assert_geodataframe_equal(element_dict["values_polygons"], sdata["values_polygons"])
+    elif join_type == "right":
+        # table check
+        assert_anndata_equal(table.obs, sdata["table"].obs)
+        # shapes check
+        assert_geodataframe_equal(element_dict["values_circles"], sdata["values_circles"])
+        assert_geodataframe_equal(element_dict["values_polygons"], sdata["values_polygons"])
+    elif join_type == "left_exclusive":
+        # TODO: currently not working, reported in this issue
+        pass
+    else:
+        assert join_type == "right_exclusive"
+        # table check
+        assert table.n_obs == sdata["table"].n_obs - len(sdata["values_circles"]) - len(sdata["values_polygons"])
+        # shapes check
+        assert element_dict["values_circles"] is None
+        assert element_dict["values_polygons"] is None
+
+
 # TODO: there is a lot of dublicate code, simplify with a function that tests both the case sdata=None and sdata=sdata
 def test_match_rows_join(sdata_query_aggregation):
     sdata = sdata_query_aggregation