napistu 0.2.5.dev7__py3-none-any.whl → 0.3.1__py3-none-any.whl

tests/test_matching_mount.py

@@ -0,0 +1,305 @@
+import copy
+import numpy as np
+import pandas as pd
+import pytest
+from datetime import datetime
+
+from napistu.matching import mount
+from napistu.constants import IDENTIFIERS, SBML_DFS, ONTOLOGIES
+from napistu.matching.constants import (
+    FEATURE_ID_VAR_DEFAULT,
+    RESOLVE_MATCHES_AGGREGATORS,
+)
+
+
+def test_bind_wide_results(sbml_dfs_glucose_metabolism):
+    """
+    Test that bind_wide_results correctly matches identifiers and adds results to species data.
+    """
+    # Get species identifiers, excluding reactome
+    species_identifiers = (
+        sbml_dfs_glucose_metabolism.get_identifiers(SBML_DFS.SPECIES)
+        .query("bqb == 'BQB_IS'")
+        .query("ontology != 'reactome'")
+    )
+
+    # Create example data with identifiers and results
+    example_data = species_identifiers.groupby("ontology").head(10)[
+        [IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER]
+    ]
+    example_data["results_a"] = np.random.randn(len(example_data))
+    example_data["results_b"] = np.random.randn(len(example_data))
+    example_data[FEATURE_ID_VAR_DEFAULT] = range(0, len(example_data))
+
+    # Create wide format data
+    example_data_wide = (
+        example_data.pivot(
+            columns=IDENTIFIERS.ONTOLOGY,
+            values=IDENTIFIERS.IDENTIFIER,
+            index=[FEATURE_ID_VAR_DEFAULT, "results_a", "results_b"],
+        )
+        .reset_index()
+        .rename_axis(None, axis=1)
+    )
+
+    # Test inplace=False (default)
+    results_name = "test_results"
+    original_sbml_dfs = copy.deepcopy(sbml_dfs_glucose_metabolism)
+    sbml_dfs_result = mount.bind_wide_results(
+        sbml_dfs=sbml_dfs_glucose_metabolism,
+        results_df=example_data_wide,
+        results_name=results_name,
+        ontologies={ONTOLOGIES.UNIPROT, ONTOLOGIES.CHEBI},
+        dogmatic=False,
+        species_identifiers=None,
+        feature_id_var=FEATURE_ID_VAR_DEFAULT,
+        verbose=True,
+        inplace=False,
+    )
+
+    # Verify original object is unchanged
+    assert results_name not in original_sbml_dfs.species_data
+
+    # Verify the results were added correctly to the new object
+    assert results_name in sbml_dfs_result.species_data
+    bound_results = sbml_dfs_result.species_data[results_name]
+    assert set(bound_results.columns) == {
+        FEATURE_ID_VAR_DEFAULT,
+        "results_a",
+        "results_b",
+    }
+    assert bound_results.shape == (23, 3)
+    assert bound_results.loc["S00000056", "feature_id"] == "18,19"
+    assert bound_results.loc["S00000057", "feature_id"] == "18"
+    assert bound_results.loc["S00000010", "feature_id"] == "9"
+
+    # Test inplace=True
+    results_name_2 = "test_results_2"
+    sbml_dfs_inplace = copy.deepcopy(sbml_dfs_glucose_metabolism)
+    result_inplace = mount.bind_wide_results(
+        sbml_dfs=sbml_dfs_inplace,
+        results_df=example_data_wide,
+        results_name=results_name_2,
+        ontologies={ONTOLOGIES.UNIPROT, ONTOLOGIES.CHEBI},
+        dogmatic=False,
+        species_identifiers=None,
+        feature_id_var=FEATURE_ID_VAR_DEFAULT,
+        verbose=True,
+        inplace=True,
+    )
+
+    # Verify the object was modified and function returned None
+    assert result_inplace is None
+    assert results_name_2 in sbml_dfs_inplace.species_data
+
+
+def test_resolve_matches_with_example_data():
+    """Test resolve_matches function with example data for all aggregation methods."""
+    # Setup example data with overlapping 1-to-many and many-to-1 cases
+    example_data = pd.DataFrame(
+        {
+            FEATURE_ID_VAR_DEFAULT: ["A", "B", "C", "D", "D", "E", "B", "B", "C"],
+            SBML_DFS.S_ID: [
+                "s_id_1",
+                "s_id_1",
+                "s_id_1",
+                "s_id_4",
+                "s_id_5",
+                "s_id_6",
+                "s_id_2",
+                "s_id_3",
+                "s_id_3",
+            ],
+            "results_a": [1, 2, 3, 0.4, 5, 6, 0.7, 0.8, 9],
+            "results_b": [
+                "foo",
+                "foo",
+                "bar",
+                "bar",
+                "baz",
+                "baz",
+                "not",
+                "not",
+                "not",
+            ],
+        }
+    )
+
+    # Test that missing feature_id raises KeyError
+    data_no_id = pd.DataFrame(
+        {
+            SBML_DFS.S_ID: ["s_id_1", "s_id_1", "s_id_2"],
+            "results_a": [1, 2, 3],
+            "results_b": ["foo", "bar", "baz"],
+        }
+    )
+    with pytest.raises(KeyError, match=FEATURE_ID_VAR_DEFAULT):
+        mount.resolve_matches(data_no_id)
+
+    # Test with keep_id_col=True (default)
+    result_with_id = mount.resolve_matches(
+        example_data, keep_id_col=True, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.MEAN
+    )
+
+    # Verify feature_id column is present and correctly aggregated
+    assert FEATURE_ID_VAR_DEFAULT in result_with_id.columns
+    assert result_with_id.loc["s_id_1", FEATURE_ID_VAR_DEFAULT] == "A,B,C"
+    assert result_with_id.loc["s_id_3", FEATURE_ID_VAR_DEFAULT] == "B,C"
+
+    # Test with keep_id_col=False
+    result_without_id = mount.resolve_matches(
+        example_data, keep_id_col=False, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.MEAN
+    )
+
+    # Verify feature_id column is not in output
+    assert FEATURE_ID_VAR_DEFAULT not in result_without_id.columns
+
+    # Verify other columns are still present and correctly aggregated
+    assert "results_a" in result_without_id.columns
+    assert "results_b" in result_without_id.columns
+    assert "feature_id_match_count" in result_without_id.columns
+
+    # Verify numeric aggregation still works
+    actual_mean = result_without_id.loc["s_id_1", "results_a"]
+    expected_mean = 2.0  # (1 + 2 + 3) / 3
+    assert (
+        actual_mean == expected_mean
+    ), f"Expected mean {expected_mean}, but got {actual_mean}"
+
+    # Verify string aggregation still works
+    assert result_without_id.loc["s_id_1", "results_b"] == "bar,foo"
+
+    # Verify match counts are still present
+    assert result_without_id.loc["s_id_1", "feature_id_match_count"] == 3
+    assert result_without_id.loc["s_id_3", "feature_id_match_count"] == 2
+
+    # Test maximum aggregation
+    max_result = mount.resolve_matches(
+        example_data, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.MAX
+    )
+
+    # Verify maximum values are correct
+    assert max_result.loc["s_id_1", "results_a"] == 3.0  # max of [1, 2, 3]
+    assert max_result.loc["s_id_3", "results_a"] == 9.0  # max of [0.8, 9]
+    assert max_result.loc["s_id_4", "results_a"] == 0.4  # single value
+    assert max_result.loc["s_id_5", "results_a"] == 5.0  # single value
+    assert max_result.loc["s_id_6", "results_a"] == 6.0  # single value
+
+    # Test weighted mean (feature_id is used for weights regardless of keep_id_col)
+    weighted_result = mount.resolve_matches(
+        example_data,
+        numeric_agg=RESOLVE_MATCHES_AGGREGATORS.WEIGHTED_MEAN,
+        keep_id_col=True,
+    )
+
+    # For s_id_1:
+    # A appears once in total (weight = 1/1)
+    # B appears three times in total (weight = 1/3)
+    # C appears twice in total (weight = 1/2)
+    # Sum of unnormalized weights = 1 + 1/3 + 1/2 = 1.833
+    # Normalized weights:
+    # A: (1/1)/1.833 = 0.545
+    # B: (1/3)/1.833 = 0.182
+    # C: (1/2)/1.833 = 0.273
+    # Weighted mean = 1×0.545 + 2×0.182 + 3×0.273 = 1.73
+    actual_weighted_mean_1 = weighted_result.loc["s_id_1", "results_a"]
+    expected_weighted_mean_1 = 1.73
+    assert (
+        abs(actual_weighted_mean_1 - expected_weighted_mean_1) < 0.01
+    ), f"s_id_1 weighted mean: expected {expected_weighted_mean_1:.3f}, but got {actual_weighted_mean_1:.3f}"
+
+    # For s_id_3:
+    # B appears three times in total (weight = 1/3)
+    # C appears twice in total (weight = 1/2)
+    # Sum of unnormalized weights = 1/3 + 1/2 = 0.833
+    # Normalized weights:
+    # B: (1/3)/0.833 = 0.4
+    # C: (1/2)/0.833 = 0.6
+    # Weighted mean = 0.8×0.4 + 9×0.6 = 5.72
+    actual_weighted_mean_3 = weighted_result.loc["s_id_3", "results_a"]
+    expected_weighted_mean_3 = 5.72
+    assert (
+        abs(actual_weighted_mean_3 - expected_weighted_mean_3) < 0.01
+    ), f"s_id_3 weighted mean: expected {expected_weighted_mean_3:.3f}, but got {actual_weighted_mean_3:.3f}"
+
+    # Test weighted mean with keep_id_col=False (weights still use feature_id)
+    weighted_result_no_id = mount.resolve_matches(
+        example_data,
+        numeric_agg=RESOLVE_MATCHES_AGGREGATORS.WEIGHTED_MEAN,
+        keep_id_col=False,
+    )
+
+    # Verify weighted means are the same regardless of keep_id_col
+    assert (
+        abs(weighted_result_no_id.loc["s_id_1", "results_a"] - expected_weighted_mean_1)
+        < 0.01
+    ), "Weighted mean should be the same regardless of keep_id_col"
+    assert (
+        abs(weighted_result_no_id.loc["s_id_3", "results_a"] - expected_weighted_mean_3)
+        < 0.01
+    ), "Weighted mean should be the same regardless of keep_id_col"
+
+    # Test that both versions preserve the same index structure
+    expected_index = pd.Index(
+        ["s_id_1", "s_id_2", "s_id_3", "s_id_4", "s_id_5", "s_id_6"], name="s_id"
+    )
+    pd.testing.assert_index_equal(result_with_id.index, expected_index)
+    pd.testing.assert_index_equal(result_without_id.index, expected_index)
+
+
+def test_resolve_matches_invalid_dtypes():
+    """Test that resolve_matches raises an error for unsupported dtypes."""
+    # Setup data with boolean and datetime columns
+    data = pd.DataFrame(
+        {
+            FEATURE_ID_VAR_DEFAULT: ["A", "B", "B", "C"],
+            "bool_col": [True, False, True, False],
+            "datetime_col": [
+                datetime(2024, 1, 1),
+                datetime(2024, 1, 2),
+                datetime(2024, 1, 3),
+                datetime(2024, 1, 4),
+            ],
+            "s_id": ["s1", "s1", "s2", "s2"],
+        }
+    )
+
+    # Should raise TypeError for unsupported dtypes
+    with pytest.raises(TypeError, match="Unsupported data types"):
+        mount.resolve_matches(data)
+
+
+def test_resolve_matches_first_method():
+    """Test resolve_matches with first method."""
+    # Setup data with known order
+    data = pd.DataFrame(
+        {
+            FEATURE_ID_VAR_DEFAULT: ["A", "C", "B", "B", "A"],
+            SBML_DFS.S_ID: ["s1", "s1", "s1", "s2", "s2"],
+            "value": [1, 2, 3, 4, 5],
+        }
+    )
+
+    result = mount.resolve_matches(data, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.FIRST)
+
+    # Should take first value after sorting by feature_id
+    assert result.loc["s1", "value"] == 1  # A comes first
+    assert result.loc["s2", "value"] == 5  # A comes first
+
+
+def test_resolve_matches_deduplicate_feature_id_within_sid():
+    """Test that only the first value for each (s_id, feature_id) is used in mean aggregation."""
+    data = pd.DataFrame(
+        {
+            FEATURE_ID_VAR_DEFAULT: ["A", "A", "B"],
+            SBML_DFS.S_ID: ["s1", "s1", "s1"],
+            "value": [
+                1,
+                1,
+                2,
+            ],  # average should be 1.5 because the two A's are redundant
+        }
+    )
+
+    result = mount.resolve_matches(data, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.MEAN)
+    assert result.loc["s1", "value"] == 1.5

tests/test_matching_species.py

@@ -0,0 +1,394 @@
+import numpy as np
+import pandas as pd
+import pytest
+
+from napistu.matching.constants import FEATURE_ID_VAR_DEFAULT
+from napistu.matching.species import (
+    match_features_to_wide_pathway_species,
+    match_by_ontology_and_identifier,
+    _validate_wide_ontologies,
+    _ensure_feature_id_var,
+    features_to_pathway_species,
+)
+
+
+def test_features_to_pathway_species(sbml_dfs):
+    species_identifiers = sbml_dfs.get_identifiers("species")
+    feature_identifiers = pd.DataFrame({"chebis": ["17627", "15379", "29105", "-1"]})
+
+    matching_df = (
+        features_to_pathway_species(
+            feature_identifiers, species_identifiers, {"chebi"}, "chebis"
+        )
+        .value_counts("identifier")
+        .sort_index()
+    )
+
+    assert matching_df.index.tolist() == ["15379", "17627", "29105"]
+    assert matching_df.tolist() == [2, 3, 2]
+
+
+def test_features_to_pathway_species_basic_and_expansion():
+
+    # Mock species_identifiers table
+    species_identifiers = pd.DataFrame(
+        {
+            "ontology": ["chebi", "chebi", "uniprot", "uniprot"],
+            "identifier": ["A", "B", "X", "Y"],
+            "s_id": [1, 2, 3, 4],
+            "s_name": ["foo", "bar", "baz", "qux"],
+            "bqb": ["BQB_IS", "BQB_IS", "BQB_IS", "BQB_IS"],
+        }
+    )
+    # Basic: no expansion, single identifier per row
+    features = pd.DataFrame({"my_id": ["A", "B", "X"], "other_col": [10, 20, 30]})
+    result = features_to_pathway_species(
+        feature_identifiers=features,
+        species_identifiers=species_identifiers,
+        ontologies={"chebi", "uniprot"},
+        feature_identifiers_var="my_id",
+        expand_identifiers=False,
+    )
+    # Should map all three
+    assert set(result["my_id"]) == {"A", "B", "X"}
+    assert set(result["identifier"]) == {"A", "B", "X"}
+    assert set(result["s_name"]) == {"foo", "bar", "baz"}
+    # Expansion: one row with multiple IDs
+    features2 = pd.DataFrame({"my_id": ["A / B / X", "Y"], "other_col": [100, 200]})
+    result2 = features_to_pathway_species(
+        feature_identifiers=features2,
+        species_identifiers=species_identifiers,
+        ontologies={"chebi", "uniprot"},
+        feature_identifiers_var="my_id",
+        expand_identifiers=True,
+        identifier_delimiter="/",
+    )
+    # Should expand to 4 rows (A, B, X, Y)
+    assert set(result2["identifier"]) == {"A", "B", "X", "Y"}
+    assert set(result2["s_name"]) == {"foo", "bar", "baz", "qux"}
+    # Whitespace trimming
+    features3 = pd.DataFrame({"my_id": ["  A  /  B  /X  ", " Y"], "other_col": [1, 2]})
+    result3 = features_to_pathway_species(
+        feature_identifiers=features3,
+        species_identifiers=species_identifiers,
+        ontologies={"chebi", "uniprot"},
+        feature_identifiers_var="my_id",
+        expand_identifiers=True,
+        identifier_delimiter="/",
+    )
+    # Should expand and trim whitespace
+    assert set(result3["identifier"]) == {"A", "B", "X", "Y"}
+    assert set(result3["s_name"]) == {"foo", "bar", "baz", "qux"}
+
+
+def test_validate_wide_ontologies():
+    """Test the _validate_wide_ontologies function with various input types and error cases."""
+    # Setup test data
+    example_data_wide = pd.DataFrame(
+        {
+            "results": [-1.0, 0.0, 1.0],
+            "chebi": ["15377", "16810", "17925"],
+            "uniprot": ["P12345", "Q67890", "O43826"],
+        }
+    )
+
+    # Test auto-detection of ontology columns
+    assert _validate_wide_ontologies(example_data_wide) == {"chebi", "uniprot"}
+
+    # Test string input
+    assert _validate_wide_ontologies(example_data_wide, ontologies="chebi") == {"chebi"}
+
+    # Test set input
+    assert _validate_wide_ontologies(example_data_wide, ontologies={"chebi"}) == {
+        "chebi"
+    }
+    assert _validate_wide_ontologies(
+        example_data_wide, ontologies={"chebi", "uniprot"}
+    ) == {"chebi", "uniprot"}
+
+    # Test dictionary mapping for renaming
+    assert _validate_wide_ontologies(
+        example_data_wide, ontologies={"chebi": "reactome", "uniprot": "ensembl_gene"}
+    ) == {"reactome", "ensembl_gene"}
+
+    # Test error cases
+
+    # Missing column in set input (checks existence first)
+    with pytest.raises(
+        ValueError, match="Specified ontology columns not found in DataFrame:.*"
+    ):
+        _validate_wide_ontologies(example_data_wide, ontologies={"invalid_ontology"})
+
+    # Valid column name but invalid ontology
+    df_with_invalid = pd.DataFrame(
+        {
+            "results": [-1.0, 0.0, 1.0],
+            "invalid_ontology": ["a", "b", "c"],
+        }
+    )
+    with pytest.raises(ValueError, match="Invalid ontologies in set:.*"):
+        _validate_wide_ontologies(df_with_invalid, ontologies={"invalid_ontology"})
+
+    # Missing source column in mapping
+    with pytest.raises(ValueError, match="Source columns not found in DataFrame:.*"):
+        _validate_wide_ontologies(
+            example_data_wide, ontologies={"missing_column": "reactome"}
+        )
+
+    # Invalid target ontology in mapping
+    with pytest.raises(ValueError, match="Invalid ontologies in mapping:.*"):
+        _validate_wide_ontologies(
+            example_data_wide, ontologies={"chebi": "invalid_ontology"}
+        )
+
+    # DataFrame with no valid ontology columns
+    invalid_df = pd.DataFrame(
+        {"results": [-1.0, 0.0, 1.0], "col1": ["a", "b", "c"], "col2": ["d", "e", "f"]}
+    )
+    with pytest.raises(
+        ValueError, match="No valid ontology columns found in DataFrame.*"
+    ):
+        _validate_wide_ontologies(invalid_df)
+
+
+def test_ensure_feature_id_var():
+    """Test the _ensure_feature_id_var function with various input cases."""
+    # Test case 1: DataFrame already has feature_id column
+    df1 = pd.DataFrame({"feature_id": [100, 200, 300], "data": ["a", "b", "c"]})
+    result1 = _ensure_feature_id_var(df1)
+    # Should return unchanged DataFrame
+    pd.testing.assert_frame_equal(df1, result1)
+
+    # Test case 2: DataFrame missing feature_id column
+    df2 = pd.DataFrame({"data": ["x", "y", "z"]})
+    result2 = _ensure_feature_id_var(df2)
+    # Should add feature_id column with sequential integers
+    assert FEATURE_ID_VAR_DEFAULT in result2.columns
+    assert list(result2[FEATURE_ID_VAR_DEFAULT]) == [0, 1, 2]
+    assert list(result2["data"]) == ["x", "y", "z"]  # Original data preserved
+
+    # Test case 3: Custom feature_id column name
+    df3 = pd.DataFrame({"data": ["p", "q", "r"]})
+    custom_id = "custom_feature_id"
+    result3 = _ensure_feature_id_var(df3, feature_id_var=custom_id)
+    # Should add custom named feature_id column
+    assert custom_id in result3.columns
+    assert list(result3[custom_id]) == [0, 1, 2]
+    assert list(result3["data"]) == ["p", "q", "r"]  # Original data preserved
+
+    # Test case 4: Empty DataFrame
+    df4 = pd.DataFrame()
+    result4 = _ensure_feature_id_var(df4)
+    # Should handle empty DataFrame gracefully
+    assert FEATURE_ID_VAR_DEFAULT in result4.columns
+    assert len(result4) == 0
+
+
+def test_match_by_ontology_and_identifier():
+    """Test the match_by_ontology_and_identifier function with various input types."""
+    # Setup test data
+    feature_identifiers = pd.DataFrame(
+        {
+            "ontology": ["chebi", "chebi", "uniprot", "uniprot", "reactome"],
+            "identifier": ["15377", "16810", "P12345", "Q67890", "R12345"],
+            "results": [1.0, 2.0, -1.0, -2.0, 0.5],
+        }
+    )
+
+    species_identifiers = pd.DataFrame(
+        {
+            "ontology": ["chebi", "chebi", "uniprot", "uniprot", "ensembl_gene"],
+            "identifier": ["15377", "17925", "P12345", "O43826", "ENSG123"],
+            "s_id": ["s1", "s2", "s3", "s4", "s5"],
+            "s_name": ["compound1", "compound2", "protein1", "protein2", "gene1"],
+            "bqb": ["BQB_IS"] * 5,  # Add required bqb column with BQB_IS values
+        }
+    )
+
+    # Test with single ontology (string)
+    result = match_by_ontology_and_identifier(
+        feature_identifiers=feature_identifiers,
+        species_identifiers=species_identifiers,
+        ontologies="chebi",
+    )
+    assert len(result) == 1  # Only one matching chebi identifier
+    assert result.iloc[0]["identifier"] == "15377"
+    assert result.iloc[0]["results"] == 1.0
+    assert result.iloc[0]["ontology"] == "chebi"  # From species_identifiers
+    assert result.iloc[0]["s_name"] == "compound1"  # Verify join worked correctly
+    assert result.iloc[0]["bqb"] == "BQB_IS"  # Verify bqb column is preserved
+
+    # Test with multiple ontologies (set)
+    result = match_by_ontology_and_identifier(
+        feature_identifiers=feature_identifiers,
+        species_identifiers=species_identifiers,
+        ontologies={"chebi", "uniprot"},
+    )
+    assert len(result) == 2  # One chebi and one uniprot match
+    assert set(result["ontology"]) == {"chebi", "uniprot"}  # From species_identifiers
+    assert set(result["identifier"]) == {"15377", "P12345"}
+    # Verify results are correctly matched
+    chebi_row = result[result["ontology"] == "chebi"].iloc[0]
+    uniprot_row = result[result["ontology"] == "uniprot"].iloc[0]
+    assert chebi_row["results"] == 1.0
+    assert uniprot_row["results"] == -1.0
+    assert chebi_row["s_name"] == "compound1"
+    assert uniprot_row["s_name"] == "protein1"
+    assert chebi_row["bqb"] == "BQB_IS"
+    assert uniprot_row["bqb"] == "BQB_IS"
+
+    # Test with list of ontologies
+    result = match_by_ontology_and_identifier(
+        feature_identifiers=feature_identifiers,
+        species_identifiers=species_identifiers,
+        ontologies=["chebi", "uniprot"],
+    )
+    assert len(result) == 2
+    assert set(result["ontology"]) == {"chebi", "uniprot"}  # From species_identifiers
+
+    # Test with no matches
+    no_match_features = pd.DataFrame(
+        {"ontology": ["chebi"], "identifier": ["99999"], "results": [1.0]}
+    )
+    result = match_by_ontology_and_identifier(
+        feature_identifiers=no_match_features,
+        species_identifiers=species_identifiers,
+        ontologies="chebi",
+    )
+    assert len(result) == 0
+
+    # Test with empty features
+    empty_features = pd.DataFrame({"ontology": [], "identifier": [], "results": []})
+    result = match_by_ontology_and_identifier(
+        feature_identifiers=empty_features,
+        species_identifiers=species_identifiers,
+        ontologies={"chebi", "uniprot"},
+    )
+    assert len(result) == 0
+
+    # Test with invalid ontology
+    with pytest.raises(ValueError, match="Invalid ontologies specified:.*"):
+        match_by_ontology_and_identifier(
+            feature_identifiers=feature_identifiers,
+            species_identifiers=species_identifiers,
+            ontologies="invalid_ontology",
+        )
+
+    # Test with ontology not in feature_identifiers
+    result = match_by_ontology_and_identifier(
+        feature_identifiers=feature_identifiers,
+        species_identifiers=species_identifiers,
+        ontologies={"ensembl_gene"},  # Only in species_identifiers
+    )
+    assert len(result) == 0
+
+    # Test with custom feature_identifiers_var
+    feature_identifiers_custom = feature_identifiers.rename(
+        columns={"identifier": "custom_id"}
+    )
+    result = match_by_ontology_and_identifier(
+        feature_identifiers=feature_identifiers_custom,
+        species_identifiers=species_identifiers,
+        ontologies={"chebi"},
+        feature_identifiers_var="custom_id",
+    )
+    assert len(result) == 1
+    assert result.iloc[0]["custom_id"] == "15377"
+    assert result.iloc[0]["ontology"] == "chebi"  # From species_identifiers
+    assert result.iloc[0]["s_name"] == "compound1"
+    assert result.iloc[0]["bqb"] == "BQB_IS"
+
+
+def test_match_features_to_wide_pathway_species(sbml_dfs_glucose_metabolism):
+
+    def compare_frame_contents(df1, df2):
+        """
+        Compare if two DataFrames have the same content, ignoring index and column ordering.
+
+        Parameters
+        ----------
+        df1 : pd.DataFrame
+            First DataFrame to compare
+        df2 : pd.DataFrame
+            Second DataFrame to compare
+
+        Returns
+        -------
+        None
+        """
+        df1_sorted = (
+            df1.reindex(columns=sorted(df1.columns))
+            .sort_values(sorted(df1.columns))
+            .reset_index(drop=True)
+        )
+
+        df2_sorted = (
+            df2.reindex(columns=sorted(df2.columns))
+            .sort_values(sorted(df2.columns))
+            .reset_index(drop=True)
+        )
+
+        pd.testing.assert_frame_equal(df1_sorted, df2_sorted, check_like=True)
+
+        return None
+
+    species_identifiers = (
+        sbml_dfs_glucose_metabolism.get_identifiers("species")
+        .query("bqb == 'BQB_IS'")
+        .query("ontology != 'reactome'")
+    )
+
+    # create a table whose index is s_ids and columns are faux-measurements
+    example_data = species_identifiers.groupby("ontology").head(10)[
+        ["ontology", "identifier"]
+    ]
+
+    example_data["results_a"] = np.random.randn(len(example_data))
+    example_data["results_b"] = np.random.randn(len(example_data))
+    # add a feature_id column to the example_data which tracks the row of the original data
+    example_data["feature_id"] = range(0, len(example_data))
+
+    # pivot (identifier, ontology) to columns for each ontology
+    example_data_wide = (
+        example_data.pivot(
+            columns="ontology",
+            values="identifier",
+            index=["feature_id", "results_a", "results_b"],
+        )
+        .reset_index()
+        .rename_axis(None, axis=1)
+    )
+
+    # options, for matching
+    # 1. match by identifier and a set of ontologies (provided by arg).
+    matched_s_ids = features_to_pathway_species(
+        feature_identifiers=example_data.drop(columns="ontology"),
+        species_identifiers=species_identifiers,
+        ontologies={"uniprot", "chebi"},
+        feature_identifiers_var="identifier",
+    )
+
+    # 2. match by identifier and ontology.
+    matched_s_ids_w_ontologies = match_by_ontology_and_identifier(
+        feature_identifiers=example_data,
+        species_identifiers=species_identifiers,
+        ontologies={"uniprot", "chebi"},
+        feature_identifiers_var="identifier",
+    )
+
+    # 3. format wide identifier sets into a table with a single identifier column and apply strategy #2.
+    matched_s_ids_from_wide = match_features_to_wide_pathway_species(
+        example_data_wide,
+        species_identifiers,
+        ontologies={"uniprot", "chebi"},
+        feature_identifiers_var="identifier",
+    )
+
+    compare_frame_contents(
+        matched_s_ids.drop(columns="s_Source"),
+        matched_s_ids_w_ontologies.drop(columns="s_Source"),
+    )
+    compare_frame_contents(
+        matched_s_ids.drop(columns="s_Source"),
+        matched_s_ids_from_wide.drop(columns="s_Source"),
+    )