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

tests/test_igraph.py

@@ -1,367 +0,0 @@
-from __future__ import annotations
-
-import os
-import pytest
-
-import pandas as pd
-from napistu import sbml_dfs_core
-from napistu.constants import DEFAULT_WT_TRANS
-from napistu.constants import MINI_SBO_FROM_NAME
-from napistu.ingestion import sbml
-from napistu.network import neighborhoods
-from napistu.network import net_create
-from napistu.network import net_utils
-from napistu.network import paths
-
-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)
-
-# create a dict containing reaction species for a few example reactions
-reaction_species_examples_dict = dict()
-
-# stub with a random reaction
-r_id = sbml_dfs.reactions.index[0]
-
-reaction_species_examples_dict["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"])
-
-reaction_species_examples_dict["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"])
-
-
-# simple reaction with just substrates and products
-reaction_species_examples_dict["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"])
-
-reaction_species_examples_dict["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"])
-
-reaction_species_examples_dict["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"])
-
-reaction_species_examples_dict["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"])
-
-
-def test_create_cpr_graph():
-    _ = net_create.create_cpr_graph(sbml_dfs, graph_type="bipartite")
-    _ = net_create.create_cpr_graph(sbml_dfs, graph_type="regulatory")
-    _ = net_create.create_cpr_graph(sbml_dfs, graph_type="surrogate")
-
-
-def test_create_cpr_graph_none_attrs():
-    # Should not raise when reaction_graph_attrs is None
-    _ = net_create.create_cpr_graph(
-        sbml_dfs, reaction_graph_attrs=None, graph_type="bipartite"
-    )
-
-
-def test_igraph_construction():
-    _ = net_create.process_cpr_graph(sbml_dfs)
-
-
-def test_process_cpr_graph_none_attrs():
-    # Should not raise when reaction_graph_attrs is None
-    _ = net_create.process_cpr_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"]
-
-    net_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 = net_utils._create_network_save_string(
-                model_prefix="tmp",
-                outdir="/tmp",
-                directed=directed,
-                graph_type=graph_type,
-            )
-            network_graph = net_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_shortest_paths():
-    species = sbml_dfs.species
-    source_species = species[species["s_name"] == "NADH"]
-    dest_species = species[species["s_name"] == "NAD+"]
-    target_species_paths = net_utils.compartmentalize_species_pairs(
-        sbml_dfs, source_species.index.tolist(), dest_species.index.tolist()
-    )
-
-    # directed graph
-    cpr_graph = net_create.process_cpr_graph(
-        sbml_dfs, directed=True, weighting_strategy="topology"
-    )
-    (
-        all_shortest_reaction_paths_df,
-        all_shortest_reaction_path_edges_df,
-        edge_sources,
-        paths_graph,
-    ) = paths.find_all_shortest_reaction_paths(
-        cpr_graph, sbml_dfs, target_species_paths, weight_var="weights"
-    )
-
-    # undirected graph
-    cpr_graph = net_create.process_cpr_graph(
-        sbml_dfs, directed=False, weighting_strategy="topology"
-    )
-    (
-        all_shortest_reaction_paths_df,
-        all_shortest_reaction_path_edges_df,
-        edge_sources,
-        paths_graph,
-    ) = paths.find_all_shortest_reaction_paths(
-        cpr_graph, sbml_dfs, target_species_paths, weight_var="weights"
-    )
-
-    assert all_shortest_reaction_paths_df.shape[0] == 3
-
-
-def test_neighborhood():
-    species = sbml_dfs.species
-    source_species = species[species["s_name"] == "NADH"].index.tolist()
-
-    query_sc_species = net_utils.compartmentalize_species(sbml_dfs, source_species)
-    compartmentalized_species = query_sc_species["sc_id"].tolist()
-
-    cpr_graph = net_create.process_cpr_graph(
-        sbml_dfs, directed=True, weighting_strategy="topology"
-    )
-
-    neighborhood = neighborhoods.find_neighborhoods(
-        sbml_dfs,
-        cpr_graph,
-        compartmentalized_species=compartmentalized_species,
-        order=3,
-    )
-
-    assert neighborhood["species_73473"]["vertices"].shape[0] == 6
-
-
-def test_format_interactors():
-    # 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():
-    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_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"
-
-
-def test_entity_validation():
-    entity_attrs = {"table": "reactions", "variable": "foo"}
-
-    assert net_create._EntityAttrValidator(**entity_attrs).model_dump() == {
-        **entity_attrs,
-        **{"trans": DEFAULT_WT_TRANS},
-    }
-
-
-################################################
-# __main__
-################################################
-
-if __name__ == "__main__":
-    test_create_cpr_graph()
-    test_igraph_loading()
-    test_igraph_construction()
-    test_shortest_paths()
-    test_neighborhood()
-    test_format_interactors()
-    test_reverse_network_edges()
-    test_entity_validation()