napistu 0.2.5.dev7__py3-none-any.whl → 0.3.1.dev1__py3-none-any.whl

tests/test_network_net_create.py

@@ -0,0 +1,459 @@
+from __future__ import annotations
+
+import os
+import pytest
+
+import numpy as np
+import pandas as pd
+
+from napistu import sbml_dfs_core
+from napistu.ingestion import sbml
+from napistu.network import net_create
+from napistu.network import ng_utils
+from napistu.constants import MINI_SBO_FROM_NAME
+from napistu.constants import SBML_DFS
+from napistu.network.constants import DEFAULT_WT_TRANS
+from napistu.network.constants import WEIGHTING_SPEC
+
+
+test_path = os.path.abspath(os.path.join(__file__, os.pardir))
+test_data = os.path.join(test_path, "test_data")
+
+sbml_path = os.path.join(test_data, "R-HSA-1237044.sbml")
+sbml_model = sbml.SBML(sbml_path).model
+sbml_dfs = sbml_dfs_core.SBML_dfs(sbml_model)
+
+
+@pytest.fixture
+def reaction_species_examples(sbml_dfs):
+    """
+    Pytest fixture providing a dictionary of example reaction species DataFrames for various test cases.
+    """
+    r_id = sbml_dfs.reactions.index[0]
+    d = dict()
+    d["valid_interactor"] = pd.DataFrame(
+        {
+            "r_id": [r_id, r_id],
+            "sbo_term": [
+                MINI_SBO_FROM_NAME["interactor"],
+                MINI_SBO_FROM_NAME["interactor"],
+            ],
+            "sc_id": ["sc1", "sc2"],
+            "stoichiometry": [0, 0],
+        }
+    ).set_index(["r_id", "sbo_term"])
+    d["invalid_interactor"] = pd.DataFrame(
+        {
+            "r_id": [r_id, r_id],
+            "sbo_term": [
+                MINI_SBO_FROM_NAME["interactor"],
+                MINI_SBO_FROM_NAME["product"],
+            ],
+            "sc_id": ["sc1", "sc2"],
+            "stoichiometry": [0, 0],
+        }
+    ).set_index(["r_id", "sbo_term"])
+    d["sub_and_prod"] = pd.DataFrame(
+        {
+            "r_id": [r_id, r_id],
+            "sbo_term": [MINI_SBO_FROM_NAME["reactant"], MINI_SBO_FROM_NAME["product"]],
+            "sc_id": ["sub", "prod"],
+            "stoichiometry": [-1, 1],
+        }
+    ).set_index(["r_id", "sbo_term"])
+    d["stimulator"] = pd.DataFrame(
+        {
+            "r_id": [r_id, r_id, r_id],
+            "sbo_term": [
+                MINI_SBO_FROM_NAME["reactant"],
+                MINI_SBO_FROM_NAME["product"],
+                MINI_SBO_FROM_NAME["stimulator"],
+            ],
+            "sc_id": ["sub", "prod", "stim"],
+            "stoichiometry": [-1, 1, 0],
+        }
+    ).set_index(["r_id", "sbo_term"])
+    d["all_entities"] = pd.DataFrame(
+        {
+            "r_id": [r_id, r_id, r_id, r_id],
+            "sbo_term": [
+                MINI_SBO_FROM_NAME["reactant"],
+                MINI_SBO_FROM_NAME["product"],
+                MINI_SBO_FROM_NAME["stimulator"],
+                MINI_SBO_FROM_NAME["catalyst"],
+            ],
+            "sc_id": ["sub", "prod", "stim", "cat"],
+            "stoichiometry": [-1, 1, 0, 0],
+        }
+    ).set_index(["r_id", "sbo_term"])
+    d["no_substrate"] = pd.DataFrame(
+        {
+            "r_id": [r_id, r_id, r_id, r_id, r_id],
+            "sbo_term": [
+                MINI_SBO_FROM_NAME["product"],
+                MINI_SBO_FROM_NAME["stimulator"],
+                MINI_SBO_FROM_NAME["stimulator"],
+                MINI_SBO_FROM_NAME["inhibitor"],
+                MINI_SBO_FROM_NAME["catalyst"],
+            ],
+            "sc_id": ["prod", "stim1", "stim2", "inh", "cat"],
+            "stoichiometry": [1, 0, 0, 0, 0],
+        }
+    ).set_index(["r_id", "sbo_term"])
+
+    return r_id, d
+
+
+def test_create_napistu_graph():
+    _ = net_create.create_napistu_graph(sbml_dfs, graph_type="bipartite")
+    _ = net_create.create_napistu_graph(sbml_dfs, graph_type="regulatory")
+    _ = net_create.create_napistu_graph(sbml_dfs, graph_type="surrogate")
+
+
+def test_create_napistu_graph_edge_reversed():
+    """Test that edge_reversed=True properly reverses edges in the graph for all graph types."""
+    # Test each graph type
+    for graph_type in ["bipartite", "regulatory", "surrogate"]:
+        # Create graphs with and without edge reversal
+        normal_graph = net_create.create_napistu_graph(
+            sbml_dfs, graph_type=graph_type, directed=True, edge_reversed=False
+        )
+        reversed_graph = net_create.create_napistu_graph(
+            sbml_dfs, graph_type=graph_type, directed=True, edge_reversed=True
+        )
+
+        # Get edge dataframes for comparison
+        normal_edges = normal_graph.get_edge_dataframe()
+        reversed_edges = reversed_graph.get_edge_dataframe()
+
+        # Verify we have edges to test
+        assert len(normal_edges) > 0, f"No edges found in {graph_type} graph"
+        assert len(normal_edges) == len(
+            reversed_edges
+        ), f"Edge count mismatch in {graph_type} graph"
+
+        # Test edge reversal
+        # Check a few edges to verify from/to are swapped
+        for i in range(min(5, len(normal_edges))):
+            # Check from/to are swapped
+            assert (
+                normal_edges.iloc[i]["from"] == reversed_edges.iloc[i]["to"]
+            ), f"From/to not properly swapped in {graph_type} graph"
+            assert (
+                normal_edges.iloc[i]["to"] == reversed_edges.iloc[i]["from"]
+            ), f"From/to not properly swapped in {graph_type} graph"
+
+            # Check stoichiometry is negated
+            assert (
+                normal_edges.iloc[i]["stoichiometry"]
+                == -reversed_edges.iloc[i]["stoichiometry"]
+            ), f"Stoichiometry not properly negated in {graph_type} graph"
+
+            # Check direction attributes are properly swapped
+            if normal_edges.iloc[i]["direction"] == "forward":
+                assert (
+                    reversed_edges.iloc[i]["direction"] == "reverse"
+                ), f"Direction not properly reversed (forward->reverse) in {graph_type} graph"
+            elif normal_edges.iloc[i]["direction"] == "reverse":
+                assert (
+                    reversed_edges.iloc[i]["direction"] == "forward"
+                ), f"Direction not properly reversed (reverse->forward) in {graph_type} graph"
+
+            # Check parents/children are swapped
+            assert (
+                normal_edges.iloc[i]["sc_parents"]
+                == reversed_edges.iloc[i]["sc_children"]
+            ), f"Parents/children not properly swapped in {graph_type} graph"
+            assert (
+                normal_edges.iloc[i]["sc_children"]
+                == reversed_edges.iloc[i]["sc_parents"]
+            ), f"Parents/children not properly swapped in {graph_type} graph"
+
+
+def test_create_napistu_graph_none_attrs():
+    # Should not raise when reaction_graph_attrs is None
+    _ = net_create.create_napistu_graph(
+        sbml_dfs, reaction_graph_attrs=None, graph_type="bipartite"
+    )
+
+
+def test_process_napistu_graph_none_attrs():
+    # Should not raise when reaction_graph_attrs is None
+    _ = net_create.process_napistu_graph(sbml_dfs, reaction_graph_attrs=None)
+
+
+@pytest.mark.skip_on_windows
+def test_igraph_loading():
+    # test read/write of an igraph network
+    directeds = [True, False]
+    graph_types = ["bipartite", "regulatory"]
+
+    ng_utils.export_networks(
+        sbml_dfs,
+        model_prefix="tmp",
+        outdir="/tmp",
+        directeds=directeds,
+        graph_types=graph_types,
+    )
+
+    for graph_type in graph_types:
+        for directed in directeds:
+            import_pkl_path = ng_utils._create_network_save_string(
+                model_prefix="tmp",
+                outdir="/tmp",
+                directed=directed,
+                graph_type=graph_type,
+            )
+            network_graph = ng_utils.read_network_pkl(
+                model_prefix="tmp",
+                network_dir="/tmp",
+                directed=directed,
+                graph_type=graph_type,
+            )
+
+            assert network_graph.is_directed() == directed
+            # cleanup
+            os.unlink(import_pkl_path)
+
+
+def test_format_interactors(reaction_species_examples):
+    r_id, reaction_species_examples_dict = reaction_species_examples
+    # interactions are formatted
+
+    graph_hierarchy_df = net_create._create_graph_hierarchy_df("regulatory")
+
+    assert (
+        net_create._format_tiered_reaction_species(
+            r_id,
+            reaction_species_examples_dict["valid_interactor"],
+            sbml_dfs,
+            graph_hierarchy_df,
+        ).shape[0]
+        == 1
+    )
+
+    print("Re-enable test once Issue #102 is solved")
+
+    # catch error from invalid interactor specification
+    # with pytest.raises(ValueError) as excinfo:
+    #    net_create._format_tiered_reaction_species(
+    #        r_id, reaction_species_examples_dict["invalid_interactor"], sbml_dfs
+    #    )
+    # assert str(excinfo.value).startswith("Invalid combinations of SBO_terms")
+
+    # simple reaction with just substrates and products
+    assert (
+        net_create._format_tiered_reaction_species(
+            r_id,
+            reaction_species_examples_dict["sub_and_prod"],
+            sbml_dfs,
+            graph_hierarchy_df,
+        ).shape[0]
+        == 2
+    )
+
+    # add a stimulator (activator)
+    rxn_edges = net_create._format_tiered_reaction_species(
+        r_id, reaction_species_examples_dict["stimulator"], sbml_dfs, graph_hierarchy_df
+    )
+
+    assert rxn_edges.shape[0] == 3
+    assert rxn_edges.iloc[0][["from", "to"]].tolist() == ["stim", "sub"]
+
+    # add catalyst + stimulator
+    rxn_edges = net_create._format_tiered_reaction_species(
+        r_id,
+        reaction_species_examples_dict["all_entities"],
+        sbml_dfs,
+        graph_hierarchy_df,
+    )
+
+    assert rxn_edges.shape[0] == 4
+    assert rxn_edges.iloc[0][["from", "to"]].tolist() == ["stim", "cat"]
+    assert rxn_edges.iloc[1][["from", "to"]].tolist() == ["cat", "sub"]
+
+    # no substrate
+    rxn_edges = net_create._format_tiered_reaction_species(
+        r_id,
+        reaction_species_examples_dict["no_substrate"],
+        sbml_dfs,
+        graph_hierarchy_df,
+    )
+
+    assert rxn_edges.shape[0] == 5
+    # stimulator -> reactant
+    assert rxn_edges.iloc[0][["from", "to"]].tolist() == ["stim1", "cat"]
+    assert rxn_edges.iloc[1][["from", "to"]].tolist() == ["stim2", "cat"]
+    assert rxn_edges.iloc[2][["from", "to"]].tolist() == ["inh", "cat"]
+
+    # use the surrogate model tiered layout also
+
+    graph_hierarchy_df = net_create._create_graph_hierarchy_df("surrogate")
+
+    rxn_edges = net_create._format_tiered_reaction_species(
+        r_id,
+        reaction_species_examples_dict["all_entities"],
+        sbml_dfs,
+        graph_hierarchy_df,
+    )
+
+    assert rxn_edges.shape[0] == 4
+    assert rxn_edges.iloc[0][["from", "to"]].tolist() == ["stim", "sub"]
+    assert rxn_edges.iloc[1][["from", "to"]].tolist() == ["sub", "cat"]
+
+
+def test_reverse_network_edges(reaction_species_examples):
+    r_id, reaction_species_examples_dict = reaction_species_examples
+
+    graph_hierarchy_df = net_create._create_graph_hierarchy_df("regulatory")
+
+    rxn_edges = net_create._format_tiered_reaction_species(
+        r_id,
+        reaction_species_examples_dict["all_entities"],
+        sbml_dfs,
+        graph_hierarchy_df,
+    )
+    augmented_network_edges = rxn_edges.assign(r_isreversible=True)
+    augmented_network_edges["sc_parents"] = range(0, augmented_network_edges.shape[0])
+    augmented_network_edges["sc_children"] = range(
+        augmented_network_edges.shape[0], 0, -1
+    )
+
+    assert net_create._reverse_network_edges(augmented_network_edges).shape[0] == 2
+
+
+def test_entity_validation():
+    # Test basic validation
+    entity_attrs = {"table": "reactions", "variable": "foo"}
+    assert net_create._EntityAttrValidator(**entity_attrs).model_dump() == {
+        **entity_attrs,
+        **{"trans": DEFAULT_WT_TRANS},
+    }
+
+    # Test validation with custom transformations
+    custom_transformations = {
+        "nlog10": lambda x: -np.log10(x),
+        "square": lambda x: x**2,
+    }
+
+    # Test valid custom transformation
+    entity_attrs_custom = {
+        "attr1": {
+            WEIGHTING_SPEC.TABLE: "reactions",
+            WEIGHTING_SPEC.VARIABLE: "foo",
+            WEIGHTING_SPEC.TRANSFORMATION: "nlog10",
+        },
+        "attr2": {
+            WEIGHTING_SPEC.TABLE: "species",
+            WEIGHTING_SPEC.VARIABLE: "bar",
+            WEIGHTING_SPEC.TRANSFORMATION: "square",
+        },
+    }
+    # Should not raise any errors
+    net_create._validate_entity_attrs(
+        entity_attrs_custom, custom_transformations=custom_transformations
+    )
+
+    # Test invalid transformation
+    entity_attrs_invalid = {
+        "attr1": {
+            WEIGHTING_SPEC.TABLE: "reactions",
+            WEIGHTING_SPEC.VARIABLE: "foo",
+            WEIGHTING_SPEC.TRANSFORMATION: "invalid_trans",
+        }
+    }
+    with pytest.raises(ValueError) as excinfo:
+        net_create._validate_entity_attrs(
+            entity_attrs_invalid, custom_transformations=custom_transformations
+        )
+    assert "transformation 'invalid_trans' was not defined" in str(excinfo.value)
+
+    # Test with validate_transformations=False
+    # Should not raise any errors even with invalid transformation
+    net_create._validate_entity_attrs(
+        entity_attrs_invalid, validate_transformations=False
+    )
+
+    # Test with non-dict input
+    with pytest.raises(AssertionError) as excinfo:
+        net_create._validate_entity_attrs(["not", "a", "dict"])
+    assert "entity_attrs must be a dictionary" in str(excinfo.value)
+
+
+def test_pluck_entity_data_species_identity(sbml_dfs):
+    # Take first 10 species IDs
+    species_ids = sbml_dfs.species.index[:10]
+    # Create mock data with explicit dtype to ensure cross-platform consistency
+    # Fix for issue-42: Use explicit dtypes to avoid platform-specific dtype differences
+    # between Windows (int32) and macOS/Linux (int64)
+    mock_df = pd.DataFrame(
+        {
+            "string_col": [f"str_{i}" for i in range(10)],
+            "mixed_col": np.arange(-5, 5, dtype=np.int64),  # Explicitly use int64
+            "ones_col": np.ones(10, dtype=np.float64),  # Explicitly use float64
+            "squared_col": np.arange(10, dtype=np.int64),  # Explicitly use int64
+        },
+        index=species_ids,
+    )
+    # Assign to species_data
+    sbml_dfs.species_data["mock_table"] = mock_df
+
+    # Custom transformation: square
+    def square(x):
+        return x**2
+
+    custom_transformations = {"square": square}
+    # Create graph_attrs for species
+    graph_attrs = {
+        "species": {
+            "string_col": {
+                WEIGHTING_SPEC.TABLE: "mock_table",
+                WEIGHTING_SPEC.VARIABLE: "string_col",
+                WEIGHTING_SPEC.TRANSFORMATION: "identity",
+            },
+            "mixed_col": {
+                WEIGHTING_SPEC.TABLE: "mock_table",
+                WEIGHTING_SPEC.VARIABLE: "mixed_col",
+                WEIGHTING_SPEC.TRANSFORMATION: "identity",
+            },
+            "ones_col": {
+                WEIGHTING_SPEC.TABLE: "mock_table",
+                WEIGHTING_SPEC.VARIABLE: "ones_col",
+                WEIGHTING_SPEC.TRANSFORMATION: "identity",
+            },
+            "squared_col": {
+                WEIGHTING_SPEC.TABLE: "mock_table",
+                WEIGHTING_SPEC.VARIABLE: "squared_col",
+                WEIGHTING_SPEC.TRANSFORMATION: "square",
+            },
+        }
+    }
+    # Call pluck_entity_data with custom transformation
+    result = net_create.pluck_entity_data(
+        sbml_dfs, graph_attrs, "species", custom_transformations=custom_transformations
+    )
+    # Check output
+    assert isinstance(result, pd.DataFrame)
+    assert set(result.columns) == {"string_col", "mixed_col", "ones_col", "squared_col"}
+    assert list(result.index) == list(species_ids)
+    # Check values
+    pd.testing.assert_series_equal(result["string_col"], mock_df["string_col"])
+    pd.testing.assert_series_equal(result["mixed_col"], mock_df["mixed_col"])
+    pd.testing.assert_series_equal(result["ones_col"], mock_df["ones_col"])
+    pd.testing.assert_series_equal(
+        result["squared_col"], mock_df["squared_col"].apply(square)
+    )
+
+
+def test_pluck_entity_data_missing_species_key(sbml_dfs):
+    # graph_attrs does not contain 'species' key
+    graph_attrs = {}
+    result = net_create.pluck_entity_data(sbml_dfs, graph_attrs, SBML_DFS.SPECIES)
+    assert result is None
+
+
+def test_pluck_entity_data_empty_species_dict(sbml_dfs):
+    # graph_attrs contains 'species' key but value is empty dict
+    graph_attrs = {SBML_DFS.SPECIES: {}}
+    result = net_create.pluck_entity_data(sbml_dfs, graph_attrs, SBML_DFS.SPECIES)
+    assert result is None

tests/test_network_ng_utils.py

@@ -0,0 +1,30 @@
+import igraph as ig
+import pandas as pd
+
+from napistu.network import ng_utils
+from napistu.network.napistu_graph_core import NapistuGraph
+
+
+def test_napistu_graph_to_pandas_dfs():
+    graph_data = [
+        (0, 1),
+        (0, 2),
+        (2, 3),
+        (3, 4),
+        (4, 2),
+        (2, 5),
+        (5, 0),
+        (6, 3),
+        (5, 6),
+    ]
+
+    g = NapistuGraph.from_igraph(ig.Graph(graph_data, directed=True))
+    vs, es = ng_utils.napistu_graph_to_pandas_dfs(g)
+
+    assert all(vs["index"] == list(range(0, 7)))
+    assert (
+        pd.DataFrame(graph_data)
+        .rename({0: "source", 1: "target"}, axis=1)
+        .sort_values(["source", "target"])
+        .equals(es.sort_values(["source", "target"]))
+    )

tests/test_network_paths.py

@@ -0,0 +1,56 @@
+import pandas as pd
+
+from napistu.network import paths
+from napistu.network import ng_utils
+
+
+def test_shortest_paths(sbml_dfs, napistu_graph, napistu_graph_undirected):
+    species = sbml_dfs.species
+    source_species = species[species["s_name"] == "NADH"]
+    dest_species = species[species["s_name"] == "NAD+"]
+    target_species_paths = ng_utils.compartmentalize_species_pairs(
+        sbml_dfs, source_species.index.tolist(), dest_species.index.tolist()
+    )
+
+    (
+        all_shortest_reaction_paths_df,
+        _,
+        _,
+        _,
+    ) = paths.find_all_shortest_reaction_paths(
+        napistu_graph, sbml_dfs, target_species_paths, weight_var="weights"
+    )
+
+    # undirected graph
+    (
+        all_shortest_reaction_paths_df,
+        all_shortest_reaction_path_edges_df,
+        edge_sources,
+        paths_graph,
+    ) = paths.find_all_shortest_reaction_paths(
+        napistu_graph_undirected, sbml_dfs, target_species_paths, weight_var="weights"
+    )
+
+    assert all_shortest_reaction_paths_df.shape[0] == 3
+
+
+def test_net_polarity():
+    polarity_series = pd.Series(
+        ["ambiguous", "ambiguous"], index=[0, 1], name="link_polarity"
+    )
+    assert all(
+        [x == "ambiguous" for x in paths._calculate_net_polarity(polarity_series)]
+    )
+
+    polarity_series = pd.Series(
+        ["activation", "inhibition", "inhibition", "ambiguous"],
+        index=range(0, 4),
+        name="link_polarity",
+    )
+    assert paths._calculate_net_polarity(polarity_series) == [
+        "activation",
+        "inhibition",
+        "activation",
+        "ambiguous activation",
+    ]
+    assert paths._terminal_net_polarity(polarity_series) == "ambiguous activation"

tests/{test_precomputed_distances.py → test_network_precompute.py}

@@ -20,7 +20,7 @@ sbml_model = sbml.SBML(sbml_path).model
 sbml_dfs = sbml_dfs_core.SBML_dfs(sbml_model)
 sbml_dfs.validate()
 
-cpr_graph = net_create.process_cpr_graph(
+napistu_graph = net_create.process_napistu_graph(
     sbml_dfs, graph_type="bipartite", directed=True, weighting_strategy="topology"
 )
 
@@ -33,7 +33,7 @@ ORDER = 20
 TOP_N = 20
 
 precomputed_distances = precompute.precompute_distances(
-    cpr_graph, max_steps=30000, max_score_q=1
+    napistu_graph, max_steps=30000, max_score_q=1
 )
 
 
@@ -55,7 +55,9 @@ def test_precomputed_distances_shortest_paths():
         _,
         _,
         _,
-    ) = paths.find_all_shortest_reaction_paths(cpr_graph, sbml_dfs, all_species_pairs)
+    ) = paths.find_all_shortest_reaction_paths(
+        napistu_graph, sbml_dfs, all_species_pairs
+    )
 
     shortest_path_weights = (
         path_vertices.groupby(["origin", "dest", "path"])["weights"]
@@ -101,7 +103,7 @@ def test_precomputed_distances_shortest_paths():
 
     # using the precomputed distances generates the same result as excluding it
     (precompute_path_vertices, _, _, _) = paths.find_all_shortest_reaction_paths(
-        cpr_graph,
+        napistu_graph,
         sbml_dfs,
         all_species_pairs,
         precomputed_distances=precomputed_distances,
@@ -139,7 +141,7 @@ def test_precomputed_distances_neighborhoods():
 
     pruned_neighborhoods_precomputed = neighborhoods.find_and_prune_neighborhoods(
         sbml_dfs,
-        cpr_graph,
+        napistu_graph,
         compartmentalized_species,
         precomputed_distances=precomputed_distances,
         network_type=NETWORK_TYPE,
@@ -150,7 +152,7 @@ def test_precomputed_distances_neighborhoods():
 
     pruned_neighborhoods_otf = neighborhoods.find_and_prune_neighborhoods(
         sbml_dfs,
-        cpr_graph,
+        napistu_graph,
         compartmentalized_species,
         precomputed_distances=None,
         network_type=NETWORK_TYPE,

tests/test_ontologies_genodexito.py

@@ -0,0 +1,58 @@
+import pandas as pd
+from napistu.ontologies.genodexito import Genodexito
+from napistu.ontologies.constants import (
+    GENODEXITO_DEFS,
+    INTERCONVERTIBLE_GENIC_ONTOLOGIES,
+    PROTEIN_ONTOLOGIES,
+)
+
+
+def test_genodexito_mapping_operations():
+    """Test Genodexito mapping table creation and operations."""
+    # Initialize with test mode and Python method to avoid R dependencies
+    geno = Genodexito(
+        species="Saccharomyces cerevisiae",
+        preferred_method=GENODEXITO_DEFS.PYTHON,
+        allow_fallback=False,
+        test_mode=True,
+    )
+
+    # Test subset of mappings
+    test_mappings = {"ensembl_gene", "symbol", "uniprot"}
+
+    # Verify test mappings are valid
+    assert test_mappings.issubset(
+        INTERCONVERTIBLE_GENIC_ONTOLOGIES
+    ), "Test mappings must be valid ontologies"
+
+    # Create mapping tables
+    geno.create_mapping_tables(mappings=test_mappings)
+
+    # Verify mappings were created
+    assert geno.mappings is not None, "Mappings should be created"
+    assert geno.mapper_used == GENODEXITO_DEFS.PYTHON, "Should use Python mapper"
+    assert test_mappings.issubset(
+        set(geno.mappings.keys())
+    ), "All requested mappings should be present"
+
+    # Test merge_mappings
+    geno.merge_mappings(test_mappings)
+    assert isinstance(
+        geno.merged_mappings, pd.DataFrame
+    ), "merge_mappings should create a DataFrame"
+    assert not geno.merged_mappings.empty, "Merged mappings should not be empty"
+    assert (
+        set(geno.merged_mappings.columns) & test_mappings == test_mappings
+    ), "Merged mappings should contain all requested ontologies"
+
+    # Test stack_mappings with protein ontologies
+    protein_test_mappings = set(PROTEIN_ONTOLOGIES) & test_mappings
+    if protein_test_mappings:  # Only test if we have protein ontologies
+        geno.stack_mappings(protein_test_mappings)
+        assert isinstance(
+            geno.stacked_mappings, pd.DataFrame
+        ), "stack_mappings should create a DataFrame"
+        assert not geno.stacked_mappings.empty, "Stacked mappings should not be empty"
+        assert (
+            set(geno.stacked_mappings["ontology"].unique()) == protein_test_mappings
+        ), "Stacked mappings should contain all requested protein ontologies"