test_ncbi_taxonomy

python.tests.ncbi_taxonomy.test_ncbi_taxonomy

Unit testing of :mod:ncbi_taxonomy module.

Typical usage example::

$ pytest test_ncbi_taxonomy.py

TestNCBITaxonomyUtils

Tests :class:~ensembl.ncbi_taxonomy.api.utils.Taxonomy in utils.py

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("test_dbs", [[{"src": "ncbi_db"}]], indirect=True)
class TestNCBITaxonomyUtils:
    """Tests :class:`~ensembl.ncbi_taxonomy.api.utils.Taxonomy` in utils.py"""

    dbc: UnitTestDB = None

    @pytest.fixture(scope="class", autouse=True)
    def setup(self, test_dbs: dict[str, UnitTestDB]) -> None:
        """Loads the required fixtures and values as class attributes.

        Args:
            db: Generator of unit test database (fixture).
        """
        type(self).dbc = test_dbs["ncbi_db"].dbc

    result_dict = {
        "taxon_id": 9615,
        "name": "beagle dog",
        "name_class": "includes",
        "parent_id": 9612,
        "rank": "subspecies",
        "genbank_hidden_flag": 1,
        "left_index": 595,
        "right_index": 596,
        "root_id": 1,
    }

    @pytest.mark.parametrize("taxon_id, expectation", [(9615, result_dict)])
    def test_fetch_node_by_id(self, taxon_id: int, expectation: NCBITaxonomy) -> None:
        """Tests :func:`fetch_node_by_id()`

        Args:
            taxon_id: An existing taxon_id as in ncbi_taxonomy.
            expectation: NCBITaxonomy object.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.fetch_node_by_id(session, taxon_id)
            result = result.__dict__
            result.pop("_sa_instance_state")
            assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(9616, raises(NoResultFound))])
    def test_fetch_node_by_id_false_id(self, taxon_id: int, expectation: ContextManager) -> None:
        """Tests :func:`fetch_node_by_id()` with a non-existant taxon_id.

        Args:
            taxon_id: A taxon_id that is not in ncbi_taxonomy.
            expectation: NoResultFound() exception.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                result = Taxonomy.fetch_node_by_id(session, taxon_id)
                assert result == expectation

    result_dict2 = {
        "taxon_id": 9615,
        "name": "Canis lupus familiaris",
        "name_class": "scientific name",
        "parent_id": 9612,
        "rank": "subspecies",
        "genbank_hidden_flag": 1,
        "left_index": 595,
        "right_index": 596,
        "root_id": 1,
    }

    @pytest.mark.parametrize("name, expectation", [("Canis lupus familiaris", result_dict2)])
    def test_fetch_taxon_by_species_name(self, name: int, expectation: NCBITaxonomy) -> None:
        """Tests :func:`fetch_taxon_by_species_name()`.

        Args:
            name: An existing scientific name as in ncbi_taxonomy.
            expectation: Class NCBITaxonomy object.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.fetch_taxon_by_species_name(session, name)
            result = result.__dict__
            result.pop("_sa_instance_state")
            assert result == expectation

    @pytest.mark.parametrize("name, expectation", [("Canis loopy familiaris", raises(NoResultFound))])
    def test_fetch_taxon_by_species_name_false_name(self, name: int, expectation: ContextManager) -> None:
        """Tests :func:`fetch_taxon_by_species_name()` with a non-existant name.

        Args:
            name: A false scientific name not in ncbi_taxonomy.
            expectation: NoResultFound() exception.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                result = Taxonomy.fetch_taxon_by_species_name(session, name)
                assert result == expectation

    result_dict3 = {
        "taxon_id": 9612,
        "name": "Canis lupus",
        "name_class": "scientific name",
        "parent_id": 9611,
        "rank": "species",
        "genbank_hidden_flag": 1,
        "left_index": 594,
        "right_index": 597,
        "root_id": 1,
    }

    @pytest.mark.parametrize("taxon_id, expectation", [(9615, result_dict3)])
    def test_parent(self, taxon_id: int, expectation: NCBITaxonomy) -> None:
        """Tests :func:`parent()`.

        Args:
            taxon_id: An existing taxon_id as in ncbi_taxonomy.
            expectation: Class NCBITaxonomy object.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.parent(session, taxon_id)
            result = result.__dict__
            result.pop("_sa_instance_state")
            assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(9616, raises(NoResultFound))])
    def test_parent_false_id(self, taxon_id: int, expectation: ContextManager) -> None:
        """Tests :func:`parent()` with non-existant taxon_id.

        Args:
            taxon_id: A false taxon_id not in ncbi_taxonomy.
            expectation: NoResultFound() exception.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                result = Taxonomy.parent(session, taxon_id)
                assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(1, raises(NoResultFound))])
    def test_parent_as_root_id(self, taxon_id: int, expectation: ContextManager) -> None:
        """Tests :func:`parent()` with root taxon_id, no parent expected of course.

        Args:
            taxon_id: The root taxon_id not in ncbi_taxonomy.
            expectation: NoResultFound() exception.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                result = Taxonomy.parent(session, taxon_id)
                assert result == expectation

    result_tuple = (
        {
            "genbank_hidden_flag": 0,
            "left_index": 356,
            "name": "Hystricognathi",
            "name_class": "scientific name",
            "parent_id": 9989,
            "rank": "suborder",
            "right_index": 363,
            "root_id": 1,
            "taxon_id": 33550,
        },
        {
            "genbank_hidden_flag": 0,
            "left_index": 364,
            "name": "Sciurognathi",
            "name_class": "scientific name",
            "parent_id": 9989,
            "rank": "suborder",
            "right_index": 399,
            "root_id": 1,
            "taxon_id": 33553,
        },
    )

    @pytest.mark.parametrize("taxon_id, expectation", [(9989, result_tuple)])
    def test_children(self, taxon_id: int, expectation: tuple) -> None:
        """Tests :func:`children()`.

        Args:
            taxon_id: An existing taxon_id as in ncbi_taxonomy.
            expectation: A tuple of Class NCBITaxonomy objects.
        """
        with self.dbc.session_scope() as session:
            results = Taxonomy.children(session, taxon_id)
            rows = list(results)
            for row in rows:
                row.pop("_sa_instance_state")
            results = tuple(rows)
            assert results == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(9615, raises(NoResultFound))])
    def test_children_none(self, taxon_id: int, expectation: ContextManager) -> None:
        """Tests :func:`children()` with extant leaf taxon_id, no children expected of course.

        Args:
            taxon_id: The root taxon_id not in ncbi_taxonomy.
            expectation: NoResultFound() exception.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                results = Taxonomy.children(session, taxon_id)
                assert results == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(1, True)])
    def test_is_root(self, taxon_id: int, expectation: bool) -> None:
        """Tests :func:`is_root()`.

        Args:
            taxon_id: Root taxon_id as in ncbi_taxonomy.
            expectation: True.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.is_root(session, taxon_id)
            assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(9615, False)])
    def test_is_root_not_root(self, taxon_id: int, expectation: bool) -> None:
        """Tests :func:`is_root()` with extant leaf taxon_id, not a root.

        Args:
            taxon_id: A leaf taxon_id in ncbi_taxonomy.
            expectation: False.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.is_root(session, taxon_id)
            assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(9612, 1)])
    def test_num_descendants(self, taxon_id: int, expectation: int) -> None:
        """Tests :func:`num_descendants()`.

        Args:
            taxon_id: An internal node taxon_id in ncbi_taxonomy.
            expectation: Correct number of descendants.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.num_descendants(session, taxon_id)
            assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(1, 381)])
    def test_num_descendants_large(self, taxon_id: int, expectation: int) -> None:
        """Tests :func:`num_descendants()`.

        Args:
            taxon_id: The root node taxon_id in ncbi_taxonomy.
            expectation: The total number taxon entries in db - 1.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.num_descendants(session, taxon_id)
            assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(9615, 0)])
    def test_num_descendants_leaf_taxon(self, taxon_id: int, expectation: int) -> None:
        """Tests :func:`num_descendants()` with leaf taxon_id.

        Args:
            taxon_id: Leaf taxon_id not in ncbi_taxonomy.
            expectation: Correct number of descendants.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.num_descendants(session, taxon_id)
            assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(0, raises(NoResultFound))])
    def test_num_descendants_false_taxon(self, taxon_id: int, expectation: ContextManager) -> None:
        """Tests :func:`num_descendants()` with leaf taxon_id.

        Args:
            taxon_id: Leaf taxon_id not in ncbi_taxonomy.
            expectation: Correct number of descendants.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                result = Taxonomy.num_descendants(session, taxon_id)
                assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(9615, True)])
    def test_is_leaf(self, taxon_id: int, expectation: bool) -> None:
        """Tests :func:`is_leaf()`.

        Args:
            taxon_id: leaf taxon_id as in ncbi_taxonomy.
            expectation: True.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.is_leaf(session, taxon_id)
            assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(1, False)])
    def test_is_leaf_not_leaf(self, taxon_id: int, expectation: bool) -> None:
        """Tests :func:`is_leaf()` with root taxon_id - so not a leaf.

        Args:
            taxon_id: The root taxon_id in ncbi_taxonomy.
            expectation: False.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.is_leaf(session, taxon_id)
            assert result == expectation

    result_tuple2 = (
        {
            "genbank_hidden_flag": 0,
            "left_index": 1,
            "parent_id": 0,
            "rank": "no rank",
            "right_index": 764,
            "root_id": 1,
            "taxon_id": 1,
        },
        {
            "genbank_hidden_flag": 0,
            "left_index": 3,
            "parent_id": 131567,
            "rank": "superkingdom",
            "right_index": 762,
            "root_id": 1,
            "taxon_id": 2759,
        },
        {
            "genbank_hidden_flag": 1,
            "left_index": 4,
            "parent_id": 2759,
            "rank": "no rank",
            "right_index": 761,
            "root_id": 1,
            "taxon_id": 33154,
        },
        {
            "genbank_hidden_flag": 1,
            "left_index": 2,
            "parent_id": 1,
            "rank": "no rank",
            "right_index": 763,
            "root_id": 1,
            "taxon_id": 131567,
        },
    )

    @pytest.mark.parametrize("taxon_id, expectation", [(33208, result_tuple2)])
    def test_fetch_ancestors(self, taxon_id: int, expectation: tuple) -> None:
        """Tests :func:`fetch_ancestors()`.

        Args:
            taxon_id: An existing taxon_id as in ncbi_taxonomy.
            expectation: A tuple of dictionary from Taxonomy objects.
        """
        with self.dbc.session_scope() as session:
            results = Taxonomy.fetch_ancestors(session, taxon_id)
            rows = list(results)
            for row in rows:
                row.pop("_sa_instance_state")
            results = tuple(rows)
            assert results == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(1, raises(NoResultFound))])
    def test_fetch_ancestors_root(self, taxon_id: int, expectation: ContextManager) -> None:
        """Tests :func:`fetch_ancestors()` with root taxon_id.

        Args:
            taxon_id: The root taxon_id as in ncbi_taxonomy.
            expectation: NoResultFound() exception.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                result = Taxonomy.fetch_ancestors(session, taxon_id)
                assert result == expectation

    @pytest.mark.parametrize("taxon_id, expectation", [(0, raises(NoResultFound))])
    def test_fetch_ancestors_false_taxon(self, taxon_id: int, expectation: ContextManager) -> None:
        """Tests :func:`fetch_ancestors()` with non-existant taxon_id.

        Args:
            taxon_id: False taxon_id not in ncbi_taxonomy.
            expectation: NoResultFound() exception.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                result = Taxonomy.fetch_ancestors(session, taxon_id)
                assert result == expectation

    result_tuple3 = (
        {
            "genbank_hidden_flag": 0,
            "left_index": 1,
            "name": "all",
            "name_class": "synonym",
            "parent_id": 0,
            "rank": "no rank",
            "right_index": 764,
            "root_id": 1,
            "taxon_id": 1,
        },
        {
            "genbank_hidden_flag": 1,
            "left_index": 2,
            "name": "biota",
            "name_class": "synonym",
            "parent_id": 1,
            "rank": "no rank",
            "right_index": 763,
            "root_id": 1,
            "taxon_id": 131567,
        },
        {
            "genbank_hidden_flag": 0,
            "left_index": 3,
            "name": "Eucarya",
            "name_class": "synonym",
            "parent_id": 131567,
            "rank": "superkingdom",
            "right_index": 762,
            "root_id": 1,
            "taxon_id": 2759,
        },
        {
            "genbank_hidden_flag": 1,
            "left_index": 4,
            "name": "1500",
            "name_class": "ensembl timetree mya",
            "parent_id": 2759,
            "rank": "no rank",
            "right_index": 761,
            "root_id": 1,
            "taxon_id": 33154,
        },
    )

    @pytest.mark.parametrize("taxon_id1, taxon_id2, expectation", [(33208, 4751, result_tuple3)])
    def test_all_common_ancestors(self, taxon_id1: int, taxon_id2: int, expectation: tuple) -> None:
        """Tests :func:`all_common_ancestors()`.

        Args:
            taxon_id1: An existing taxon_id as in ncbi_taxonomy.
            taxon_id2: An existing taxon_id as in ncbi_taxonomy.
            expectation: A tuple of Class NCBITaxonomy objects.
        """
        with self.dbc.session_scope() as session:
            results = Taxonomy.all_common_ancestors(session, taxon_id1, taxon_id2)
            rows = list(results)
            result = []
            for row in rows:
                row = row.__dict__
                row.pop("_sa_instance_state")
                result.append(row)
            results = tuple(result)
            assert results == expectation

    @pytest.mark.parametrize("taxon_id1, taxon_id2, expectation", [(1, 9615, raises(NoResultFound))])
    def test_all_common_ancestors_root(
        self, taxon_id1: int, taxon_id2: int, expectation: ContextManager
    ) -> None:
        """Tests :func:`all_common_ancestors()` with leaf taxon_id.

        Args:
            taxon_id1: A root node taxon_id as in ncbi_taxonomy.
            taxon_id2: A taxon_id as in ncbi_taxonomy.
            expectation: NoResultFound() exception.
        """
        with expectation:
            with self.dbc.session_scope() as session:
                result = Taxonomy.all_common_ancestors(session, taxon_id1, taxon_id2)
                assert result == expectation

    result_dict4 = {
        "genbank_hidden_flag": 0,
        "left_index": 1,
        "name": "all",
        "name_class": "synonym",
        "parent_id": 0,
        "rank": "no rank",
        "right_index": 764,
        "root_id": 1,
        "taxon_id": 1,
    }

    @pytest.mark.parametrize("taxon_id1, taxon_id2, expectation", [(33154, 131567, result_dict4)])
    def test_last_common_ancestors(self, taxon_id1: int, taxon_id2: int, expectation: tuple) -> None:
        """Tests :func:`all_common_ancestors()`.

        Args:
            taxon_id1: An existing taxon_id as in ncbi_taxonomy.
            taxon_id2: An existing taxon_id as in ncbi_taxonomy.
            expectation: A Class NCBITaxonomy objects.
        """
        with self.dbc.session_scope() as session:
            result = Taxonomy.last_common_ancestor(session, taxon_id1, taxon_id2)
            result = result.__dict__
            result.pop("_sa_instance_state")
            assert result == expectation

dbc: UnitTestDB = None class-attribute instance-attribute

result_dict = {'taxon_id': 9615, 'name': 'beagle dog', 'name_class': 'includes', 'parent_id': 9612, 'rank': 'subspecies', 'genbank_hidden_flag': 1, 'left_index': 595, 'right_index': 596, 'root_id': 1} class-attribute instance-attribute

result_dict2 = {'taxon_id': 9615, 'name': 'Canis lupus familiaris', 'name_class': 'scientific name', 'parent_id': 9612, 'rank': 'subspecies', 'genbank_hidden_flag': 1, 'left_index': 595, 'right_index': 596, 'root_id': 1} class-attribute instance-attribute

result_dict3 = {'taxon_id': 9612, 'name': 'Canis lupus', 'name_class': 'scientific name', 'parent_id': 9611, 'rank': 'species', 'genbank_hidden_flag': 1, 'left_index': 594, 'right_index': 597, 'root_id': 1} class-attribute instance-attribute

result_dict4 = {'genbank_hidden_flag': 0, 'left_index': 1, 'name': 'all', 'name_class': 'synonym', 'parent_id': 0, 'rank': 'no rank', 'right_index': 764, 'root_id': 1, 'taxon_id': 1} class-attribute instance-attribute

result_tuple = ({'genbank_hidden_flag': 0, 'left_index': 356, 'name': 'Hystricognathi', 'name_class': 'scientific name', 'parent_id': 9989, 'rank': 'suborder', 'right_index': 363, 'root_id': 1, 'taxon_id': 33550}, {'genbank_hidden_flag': 0, 'left_index': 364, 'name': 'Sciurognathi', 'name_class': 'scientific name', 'parent_id': 9989, 'rank': 'suborder', 'right_index': 399, 'root_id': 1, 'taxon_id': 33553}) class-attribute instance-attribute

result_tuple2 = ({'genbank_hidden_flag': 0, 'left_index': 1, 'parent_id': 0, 'rank': 'no rank', 'right_index': 764, 'root_id': 1, 'taxon_id': 1}, {'genbank_hidden_flag': 0, 'left_index': 3, 'parent_id': 131567, 'rank': 'superkingdom', 'right_index': 762, 'root_id': 1, 'taxon_id': 2759}, {'genbank_hidden_flag': 1, 'left_index': 4, 'parent_id': 2759, 'rank': 'no rank', 'right_index': 761, 'root_id': 1, 'taxon_id': 33154}, {'genbank_hidden_flag': 1, 'left_index': 2, 'parent_id': 1, 'rank': 'no rank', 'right_index': 763, 'root_id': 1, 'taxon_id': 131567}) class-attribute instance-attribute

result_tuple3 = ({'genbank_hidden_flag': 0, 'left_index': 1, 'name': 'all', 'name_class': 'synonym', 'parent_id': 0, 'rank': 'no rank', 'right_index': 764, 'root_id': 1, 'taxon_id': 1}, {'genbank_hidden_flag': 1, 'left_index': 2, 'name': 'biota', 'name_class': 'synonym', 'parent_id': 1, 'rank': 'no rank', 'right_index': 763, 'root_id': 1, 'taxon_id': 131567}, {'genbank_hidden_flag': 0, 'left_index': 3, 'name': 'Eucarya', 'name_class': 'synonym', 'parent_id': 131567, 'rank': 'superkingdom', 'right_index': 762, 'root_id': 1, 'taxon_id': 2759}, {'genbank_hidden_flag': 1, 'left_index': 4, 'name': '1500', 'name_class': 'ensembl timetree mya', 'parent_id': 2759, 'rank': 'no rank', 'right_index': 761, 'root_id': 1, 'taxon_id': 33154}) class-attribute instance-attribute

setup(test_dbs)

Loads the required fixtures and values as class attributes.

Parameters:

Name	Type	Description	Default
db		Generator of unit test database (fixture).	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.fixture(scope="class", autouse=True)
def setup(self, test_dbs: dict[str, UnitTestDB]) -> None:
    """Loads the required fixtures and values as class attributes.

    Args:
        db: Generator of unit test database (fixture).
    """
    type(self).dbc = test_dbs["ncbi_db"].dbc

test_all_common_ancestors(taxon_id1, taxon_id2, expectation)

Tests :func:all_common_ancestors().

Parameters:

Name	Type	Description	Default
taxon_id1	int	An existing taxon_id as in ncbi_taxonomy.	required
taxon_id2	int	An existing taxon_id as in ncbi_taxonomy.	required
expectation	tuple	A tuple of Class NCBITaxonomy objects.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id1, taxon_id2, expectation", [(33208, 4751, result_tuple3)])
def test_all_common_ancestors(self, taxon_id1: int, taxon_id2: int, expectation: tuple) -> None:
    """Tests :func:`all_common_ancestors()`.

    Args:
        taxon_id1: An existing taxon_id as in ncbi_taxonomy.
        taxon_id2: An existing taxon_id as in ncbi_taxonomy.
        expectation: A tuple of Class NCBITaxonomy objects.
    """
    with self.dbc.session_scope() as session:
        results = Taxonomy.all_common_ancestors(session, taxon_id1, taxon_id2)
        rows = list(results)
        result = []
        for row in rows:
            row = row.__dict__
            row.pop("_sa_instance_state")
            result.append(row)
        results = tuple(result)
        assert results == expectation

test_all_common_ancestors_root(taxon_id1, taxon_id2, expectation)

Tests :func:all_common_ancestors() with leaf taxon_id.

Parameters:

Name	Type	Description	Default
taxon_id1	int	A root node taxon_id as in ncbi_taxonomy.	required
taxon_id2	int	A taxon_id as in ncbi_taxonomy.	required
expectation	ContextManager	NoResultFound() exception.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id1, taxon_id2, expectation", [(1, 9615, raises(NoResultFound))])
def test_all_common_ancestors_root(
    self, taxon_id1: int, taxon_id2: int, expectation: ContextManager
) -> None:
    """Tests :func:`all_common_ancestors()` with leaf taxon_id.

    Args:
        taxon_id1: A root node taxon_id as in ncbi_taxonomy.
        taxon_id2: A taxon_id as in ncbi_taxonomy.
        expectation: NoResultFound() exception.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            result = Taxonomy.all_common_ancestors(session, taxon_id1, taxon_id2)
            assert result == expectation

test_children(taxon_id, expectation)

Tests :func:children().

Parameters:

Name	Type	Description	Default
taxon_id	int	An existing taxon_id as in ncbi_taxonomy.	required
expectation	tuple	A tuple of Class NCBITaxonomy objects.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9989, result_tuple)])
def test_children(self, taxon_id: int, expectation: tuple) -> None:
    """Tests :func:`children()`.

    Args:
        taxon_id: An existing taxon_id as in ncbi_taxonomy.
        expectation: A tuple of Class NCBITaxonomy objects.
    """
    with self.dbc.session_scope() as session:
        results = Taxonomy.children(session, taxon_id)
        rows = list(results)
        for row in rows:
            row.pop("_sa_instance_state")
        results = tuple(rows)
        assert results == expectation

test_children_none(taxon_id, expectation)

Tests :func:children() with extant leaf taxon_id, no children expected of course.

Parameters:

Name	Type	Description	Default
taxon_id	int	The root taxon_id not in ncbi_taxonomy.	required
expectation	ContextManager	NoResultFound() exception.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9615, raises(NoResultFound))])
def test_children_none(self, taxon_id: int, expectation: ContextManager) -> None:
    """Tests :func:`children()` with extant leaf taxon_id, no children expected of course.

    Args:
        taxon_id: The root taxon_id not in ncbi_taxonomy.
        expectation: NoResultFound() exception.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            results = Taxonomy.children(session, taxon_id)
            assert results == expectation

test_fetch_ancestors(taxon_id, expectation)

Tests :func:fetch_ancestors().

Parameters:

Name	Type	Description	Default
taxon_id	int	An existing taxon_id as in ncbi_taxonomy.	required
expectation	tuple	A tuple of dictionary from Taxonomy objects.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(33208, result_tuple2)])
def test_fetch_ancestors(self, taxon_id: int, expectation: tuple) -> None:
    """Tests :func:`fetch_ancestors()`.

    Args:
        taxon_id: An existing taxon_id as in ncbi_taxonomy.
        expectation: A tuple of dictionary from Taxonomy objects.
    """
    with self.dbc.session_scope() as session:
        results = Taxonomy.fetch_ancestors(session, taxon_id)
        rows = list(results)
        for row in rows:
            row.pop("_sa_instance_state")
        results = tuple(rows)
        assert results == expectation

test_fetch_ancestors_false_taxon(taxon_id, expectation)

Tests :func:fetch_ancestors() with non-existant taxon_id.

Parameters:

Name	Type	Description	Default
taxon_id	int	False taxon_id not in ncbi_taxonomy.	required
expectation	ContextManager	NoResultFound() exception.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(0, raises(NoResultFound))])
def test_fetch_ancestors_false_taxon(self, taxon_id: int, expectation: ContextManager) -> None:
    """Tests :func:`fetch_ancestors()` with non-existant taxon_id.

    Args:
        taxon_id: False taxon_id not in ncbi_taxonomy.
        expectation: NoResultFound() exception.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            result = Taxonomy.fetch_ancestors(session, taxon_id)
            assert result == expectation

test_fetch_ancestors_root(taxon_id, expectation)

Tests :func:fetch_ancestors() with root taxon_id.

Parameters:

Name	Type	Description	Default
taxon_id	int	The root taxon_id as in ncbi_taxonomy.	required
expectation	ContextManager	NoResultFound() exception.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(1, raises(NoResultFound))])
def test_fetch_ancestors_root(self, taxon_id: int, expectation: ContextManager) -> None:
    """Tests :func:`fetch_ancestors()` with root taxon_id.

    Args:
        taxon_id: The root taxon_id as in ncbi_taxonomy.
        expectation: NoResultFound() exception.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            result = Taxonomy.fetch_ancestors(session, taxon_id)
            assert result == expectation

test_fetch_node_by_id(taxon_id, expectation)

Tests :func:fetch_node_by_id()

Parameters:

Name	Type	Description	Default
taxon_id	int	An existing taxon_id as in ncbi_taxonomy.	required
expectation	NCBITaxonomy	NCBITaxonomy object.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9615, result_dict)])
def test_fetch_node_by_id(self, taxon_id: int, expectation: NCBITaxonomy) -> None:
    """Tests :func:`fetch_node_by_id()`

    Args:
        taxon_id: An existing taxon_id as in ncbi_taxonomy.
        expectation: NCBITaxonomy object.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.fetch_node_by_id(session, taxon_id)
        result = result.__dict__
        result.pop("_sa_instance_state")
        assert result == expectation

test_fetch_node_by_id_false_id(taxon_id, expectation)

Tests :func:fetch_node_by_id() with a non-existant taxon_id.

Parameters:

Name	Type	Description	Default
taxon_id	int	A taxon_id that is not in ncbi_taxonomy.	required
expectation	ContextManager	NoResultFound() exception.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9616, raises(NoResultFound))])
def test_fetch_node_by_id_false_id(self, taxon_id: int, expectation: ContextManager) -> None:
    """Tests :func:`fetch_node_by_id()` with a non-existant taxon_id.

    Args:
        taxon_id: A taxon_id that is not in ncbi_taxonomy.
        expectation: NoResultFound() exception.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            result = Taxonomy.fetch_node_by_id(session, taxon_id)
            assert result == expectation

test_fetch_taxon_by_species_name(name, expectation)

Tests :func:fetch_taxon_by_species_name().

Parameters:

Name	Type	Description	Default
name	int	An existing scientific name as in ncbi_taxonomy.	required
expectation	NCBITaxonomy	Class NCBITaxonomy object.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("name, expectation", [("Canis lupus familiaris", result_dict2)])
def test_fetch_taxon_by_species_name(self, name: int, expectation: NCBITaxonomy) -> None:
    """Tests :func:`fetch_taxon_by_species_name()`.

    Args:
        name: An existing scientific name as in ncbi_taxonomy.
        expectation: Class NCBITaxonomy object.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.fetch_taxon_by_species_name(session, name)
        result = result.__dict__
        result.pop("_sa_instance_state")
        assert result == expectation

test_fetch_taxon_by_species_name_false_name(name, expectation)

Tests :func:fetch_taxon_by_species_name() with a non-existant name.

Parameters:

Name	Type	Description	Default
name	int	A false scientific name not in ncbi_taxonomy.	required
expectation	ContextManager	NoResultFound() exception.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("name, expectation", [("Canis loopy familiaris", raises(NoResultFound))])
def test_fetch_taxon_by_species_name_false_name(self, name: int, expectation: ContextManager) -> None:
    """Tests :func:`fetch_taxon_by_species_name()` with a non-existant name.

    Args:
        name: A false scientific name not in ncbi_taxonomy.
        expectation: NoResultFound() exception.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            result = Taxonomy.fetch_taxon_by_species_name(session, name)
            assert result == expectation

test_is_leaf(taxon_id, expectation)

Tests :func:is_leaf().

Parameters:

Name	Type	Description	Default
taxon_id	int	leaf taxon_id as in ncbi_taxonomy.	required
expectation	bool	True.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9615, True)])
def test_is_leaf(self, taxon_id: int, expectation: bool) -> None:
    """Tests :func:`is_leaf()`.

    Args:
        taxon_id: leaf taxon_id as in ncbi_taxonomy.
        expectation: True.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.is_leaf(session, taxon_id)
        assert result == expectation

test_is_leaf_not_leaf(taxon_id, expectation)

Tests :func:is_leaf() with root taxon_id - so not a leaf.

Parameters:

Name	Type	Description	Default
taxon_id	int	The root taxon_id in ncbi_taxonomy.	required
expectation	bool	False.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(1, False)])
def test_is_leaf_not_leaf(self, taxon_id: int, expectation: bool) -> None:
    """Tests :func:`is_leaf()` with root taxon_id - so not a leaf.

    Args:
        taxon_id: The root taxon_id in ncbi_taxonomy.
        expectation: False.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.is_leaf(session, taxon_id)
        assert result == expectation

test_is_root(taxon_id, expectation)

Tests :func:is_root().

Parameters:

Name	Type	Description	Default
taxon_id	int	Root taxon_id as in ncbi_taxonomy.	required
expectation	bool	True.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(1, True)])
def test_is_root(self, taxon_id: int, expectation: bool) -> None:
    """Tests :func:`is_root()`.

    Args:
        taxon_id: Root taxon_id as in ncbi_taxonomy.
        expectation: True.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.is_root(session, taxon_id)
        assert result == expectation

test_is_root_not_root(taxon_id, expectation)

Tests :func:is_root() with extant leaf taxon_id, not a root.

Parameters:

Name	Type	Description	Default
taxon_id	int	A leaf taxon_id in ncbi_taxonomy.	required
expectation	bool	False.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9615, False)])
def test_is_root_not_root(self, taxon_id: int, expectation: bool) -> None:
    """Tests :func:`is_root()` with extant leaf taxon_id, not a root.

    Args:
        taxon_id: A leaf taxon_id in ncbi_taxonomy.
        expectation: False.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.is_root(session, taxon_id)
        assert result == expectation

test_last_common_ancestors(taxon_id1, taxon_id2, expectation)

Tests :func:all_common_ancestors().

Parameters:

Name	Type	Description	Default
taxon_id1	int	An existing taxon_id as in ncbi_taxonomy.	required
taxon_id2	int	An existing taxon_id as in ncbi_taxonomy.	required
expectation	tuple	A Class NCBITaxonomy objects.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id1, taxon_id2, expectation", [(33154, 131567, result_dict4)])
def test_last_common_ancestors(self, taxon_id1: int, taxon_id2: int, expectation: tuple) -> None:
    """Tests :func:`all_common_ancestors()`.

    Args:
        taxon_id1: An existing taxon_id as in ncbi_taxonomy.
        taxon_id2: An existing taxon_id as in ncbi_taxonomy.
        expectation: A Class NCBITaxonomy objects.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.last_common_ancestor(session, taxon_id1, taxon_id2)
        result = result.__dict__
        result.pop("_sa_instance_state")
        assert result == expectation

test_num_descendants(taxon_id, expectation)

Tests :func:num_descendants().

Parameters:

Name	Type	Description	Default
taxon_id	int	An internal node taxon_id in ncbi_taxonomy.	required
expectation	int	Correct number of descendants.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9612, 1)])
def test_num_descendants(self, taxon_id: int, expectation: int) -> None:
    """Tests :func:`num_descendants()`.

    Args:
        taxon_id: An internal node taxon_id in ncbi_taxonomy.
        expectation: Correct number of descendants.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.num_descendants(session, taxon_id)
        assert result == expectation

test_num_descendants_false_taxon(taxon_id, expectation)

Tests :func:num_descendants() with leaf taxon_id.

Parameters:

Name	Type	Description	Default
taxon_id	int	Leaf taxon_id not in ncbi_taxonomy.	required
expectation	ContextManager	Correct number of descendants.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(0, raises(NoResultFound))])
def test_num_descendants_false_taxon(self, taxon_id: int, expectation: ContextManager) -> None:
    """Tests :func:`num_descendants()` with leaf taxon_id.

    Args:
        taxon_id: Leaf taxon_id not in ncbi_taxonomy.
        expectation: Correct number of descendants.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            result = Taxonomy.num_descendants(session, taxon_id)
            assert result == expectation

test_num_descendants_large(taxon_id, expectation)

Tests :func:num_descendants().

Parameters:

Name	Type	Description	Default
taxon_id	int	The root node taxon_id in ncbi_taxonomy.	required
expectation	int	The total number taxon entries in db - 1.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(1, 381)])
def test_num_descendants_large(self, taxon_id: int, expectation: int) -> None:
    """Tests :func:`num_descendants()`.

    Args:
        taxon_id: The root node taxon_id in ncbi_taxonomy.
        expectation: The total number taxon entries in db - 1.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.num_descendants(session, taxon_id)
        assert result == expectation

test_num_descendants_leaf_taxon(taxon_id, expectation)

Tests :func:num_descendants() with leaf taxon_id.

Parameters:

Name	Type	Description	Default
taxon_id	int	Leaf taxon_id not in ncbi_taxonomy.	required
expectation	int	Correct number of descendants.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9615, 0)])
def test_num_descendants_leaf_taxon(self, taxon_id: int, expectation: int) -> None:
    """Tests :func:`num_descendants()` with leaf taxon_id.

    Args:
        taxon_id: Leaf taxon_id not in ncbi_taxonomy.
        expectation: Correct number of descendants.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.num_descendants(session, taxon_id)
        assert result == expectation

test_parent(taxon_id, expectation)

Tests :func:parent().

Parameters:

Name	Type	Description	Default
taxon_id	int	An existing taxon_id as in ncbi_taxonomy.	required
expectation	NCBITaxonomy	Class NCBITaxonomy object.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9615, result_dict3)])
def test_parent(self, taxon_id: int, expectation: NCBITaxonomy) -> None:
    """Tests :func:`parent()`.

    Args:
        taxon_id: An existing taxon_id as in ncbi_taxonomy.
        expectation: Class NCBITaxonomy object.
    """
    with self.dbc.session_scope() as session:
        result = Taxonomy.parent(session, taxon_id)
        result = result.__dict__
        result.pop("_sa_instance_state")
        assert result == expectation

test_parent_as_root_id(taxon_id, expectation)

Tests :func:parent() with root taxon_id, no parent expected of course.

Parameters:

Name	Type	Description	Default
taxon_id	int	The root taxon_id not in ncbi_taxonomy.	required
expectation	ContextManager	NoResultFound() exception.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(1, raises(NoResultFound))])
def test_parent_as_root_id(self, taxon_id: int, expectation: ContextManager) -> None:
    """Tests :func:`parent()` with root taxon_id, no parent expected of course.

    Args:
        taxon_id: The root taxon_id not in ncbi_taxonomy.
        expectation: NoResultFound() exception.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            result = Taxonomy.parent(session, taxon_id)
            assert result == expectation

test_parent_false_id(taxon_id, expectation)

Tests :func:parent() with non-existant taxon_id.

Parameters:

Name	Type	Description	Default
taxon_id	int	A false taxon_id not in ncbi_taxonomy.	required
expectation	ContextManager	NoResultFound() exception.	required

Source code in src/python/tests/ncbi_taxonomy/test_ncbi_taxonomy.py

@pytest.mark.parametrize("taxon_id, expectation", [(9616, raises(NoResultFound))])
def test_parent_false_id(self, taxon_id: int, expectation: ContextManager) -> None:
    """Tests :func:`parent()` with non-existant taxon_id.

    Args:
        taxon_id: A false taxon_id not in ncbi_taxonomy.
        expectation: NoResultFound() exception.
    """
    with expectation:
        with self.dbc.session_scope() as session:
            result = Taxonomy.parent(session, taxon_id)
            assert result == expectation