test_load.py

"""Test model loading from local and remote model repositores."""

import gzip
from pathlib import Path
from typing import TYPE_CHECKING, Callable
from unittest.mock import Mock

import pytest

from cobra import Configuration
from cobra.io import BiGGModels, BioModels, EMLBGems, load_model


if TYPE_CHECKING:
    from pytest_mock import MockerFixture

    from cobra import Model


@pytest.fixture(scope="module")
def mini_sbml(cobra_data_directory: Path) -> bytes:
    """Provide a gzip-compressed SBML document."""
    with (cobra_data_directory / "mini_cobra.xml").open(mode="rb") as handle:
        return gzip.compress(handle.read())


@pytest.fixture
def bigg_models(mini_sbml: bytes, mocker: "MockerFixture") -> Mock:
    """Provide a mocked BiGG Models repository interface."""
    result = mocker.Mock(spec_set=BiGGModels)
    result.get_sbml.return_value = mini_sbml
    return result


@pytest.fixture
def biomodels(mini_sbml: bytes, mocker: "MockerFixture") -> Mock:
    """Provide a mocked BioModels repository interface."""
    result = mocker.Mock(spec_set=BioModels)
    result.get_sbml.return_value = mini_sbml
    return result

@pytest.fixture
def embl_gems(mini_sbml: bytes, mocker: "MockerFixture") -> Mock:
    """Provide a mocked EMBL Gems repository interface."""
    result = mocker.Mock(spec_set=EMLBGems)
    result.get_sbml.return_value = mini_sbml
    return result

def test_bigg_access(bigg_models: Mock) -> None:
    """Test that SBML would be retrieved from the BiGG Models repository.

    Parameters
    ----------
    bigg_models : unittest.mock.Mock
        The mocked object for BiGG model respository.

    """
    load_model("e_coli_core", cache=False, repositories=[bigg_models])
    bigg_models.get_sbml.assert_called_once_with(model_id="e_coli_core")


def test_biomodels_access(biomodels: Mock) -> None:
    """Test that SBML would be retrieved from the BioModels repository.

    Parameters
    ----------
    biomodels : unittest.mock.Mock
        The mocked object for BioModels model respository.

    """
    load_model("BIOMD0000000633", cache=False, repositories=[biomodels])
    biomodels.get_sbml.assert_called_once_with(model_id="BIOMD0000000633")


def test_biomodels_access(biomodels: Mock) -> None:
    """Test that SBML would be retrieved from the BioModels repository.

    Parameters
    ----------
    biomodels : unittest.mock.Mock
        The mocked object for BioModels model respository.

    """
    load_model("BIOMD0000000633", cache=False, repositories=[biomodels])
    biomodels.get_sbml.assert_called_once_with(model_id="BIOMD0000000633")

def test_biomodels_access(embl_gems: Mock) -> None:
    """Test that SBML would be retrieved from the EMBL Gems repository.

    Parameters
    ----------
    embl_gems : unittest.mock.Mock
        The mocked object for BioModels model respository.

    """
    load_model("Abiotrophia_defectiva_ATCC_49176", cache=False, repositories=[embl_gems])
    biomodels.get_sbml.assert_called_once_with(model_id="Abiotrophia_defectiva_ATCC_49176")

def test_unknown_model() -> None:
    """Expect that a not found error is raised (e2e)."""
    with pytest.raises(RuntimeError):
        load_model("MODELWHO?", cache=False)


@pytest.mark.parametrize(
    "model_id, num_metabolites, num_reactions",
    [("e_coli_core", 72, 95), ("BIOMD0000000633", 50, 35)],
    [("Abiotrophia_defectiva_ATCC_49176", 1070, 826)]
)
def test_remote_load(model_id: str, num_metabolites: int, num_reactions: int) -> None:
    """Test that sample models can be loaded from remote repositories (e2e).

    Parameters
    ----------
    model_id : str
        The ID of the model.
    num_metabolites : int
        The total number of metabolites in the model having ID `model_id`.
    num_reactions : int
        The total number of reactions in the model having ID `model_id`.

    """
    model = load_model(model_id, cache=False)
    assert len(model.metabolites) == num_metabolites
    assert len(model.reactions) == num_reactions


def test_cache(
    monkeypatch: pytest.MonkeyPatch, tmp_path: Path, bigg_models: Mock, biomodels: Mock
) -> None:
    """Test that remote models are properly cached.

    Parameters
    ----------
    monkeypatch : pytest.MonkeyPatch
        The monkeypatch-ing object.
    tmp_path : pathlib.Path
        The path to the temporary test assets store.
    bigg_models : Mock
        The mocked object for BiGG model respository.
    biomodels : unittest.mock.Mock
        The mocked object for BioModels model respository.

    """
    config = Configuration()
    monkeypatch.setattr(config, "cache_directory", tmp_path)
    remote_model = load_model("e_coli_core")
    cached_model = load_model("e_coli_core", repositories=[bigg_models, biomodels])
    bigg_models.get_sbml.assert_not_called()
    biomodels.get_sbml.assert_not_called()
    assert len(cached_model.metabolites) == len(remote_model.metabolites)
    assert len(cached_model.reactions) == len(remote_model.reactions)


def test_local_load(model: "Model", compare_models: Callable) -> None:
    """Test model loading from local repository.

    Parameters
    ----------
    model : cobra.Model
        The model to compare local loading against.
    compare_models : Callable
        A callable object to compare local loading.

    """
    model_local = load_model("textbook")
    compare_models(model, model_local)