test_annotation_stores.py

"""Test for annotation store classes."""

from __future__ import annotations

import json
import pickle
import sqlite3
import sys
from collections.abc import Generator
from itertools import repeat, zip_longest
from pathlib import Path
from timeit import timeit
from typing import TYPE_CHECKING, Callable, ClassVar

import numpy as np
import pandas as pd
import pytest
import shapely
from shapely import affinity
from shapely.geometry import (
    GeometryCollection,
    LineString,
    MultiLineString,
    MultiPoint,
    MultiPolygon,
    Point,
    Polygon,
)

from tiatoolbox import logger
from tiatoolbox.annotation import (
    Annotation,
    AnnotationStore,
    DictionaryStore,
    SQLiteStore,
)
from tiatoolbox.annotation.storage import SQLiteMetadata
from tiatoolbox.enums import GeometryType

if TYPE_CHECKING:  # pragma: no cover
    from numbers import Number

    from tiatoolbox.type_hints import Geometry


sqlite3.enable_callback_tracebacks(True)  # noqa: FBT003

# ----------------------------------------------------------------------
# Constants
# ----------------------------------------------------------------------

GRID_SIZE = (10, 10)
FILLED_LEN = 2 * (GRID_SIZE[0] * GRID_SIZE[1])
RNG = np.random.default_rng(0)  # Numpy Random Generator

# ----------------------------------------------------------------------
# Helper Functions
# ----------------------------------------------------------------------


def cell_polygon(
    xy: tuple[Number, Number],
    n_points: int = 20,
    radius: Number = 10,
    noise: Number = 0.01,
    eccentricity: tuple[Number, Number] = (1, 3),
    direction: str = "CCW",
    *,
    repeat_first: bool = True,
) -> Polygon:
    """Generate a fake cell boundary polygon.

    Cell boundaries are generated an ellipsoids with randomised eccentricity,
    added noise, and a random rotation.

    Args:
        xy (tuple(int)): The x,y centre point to generate the cell boundary around.
        n_points (int): Number of points in the boundary. Defaults to 20.
        radius (float): Radius of the points from the centre. Defaults to 10.
        noise (float): Noise to add to the point locations. Defaults to 1.
        eccentricity (tuple(float)): Range of values (low, high) to use for
            randomised eccentricity. Defaults to (1, 3).
        repeat_first (bool): Enforce that the last point is equal to the first.
        direction (str): Ordering of the points. Defaults to "CCW". Valid options
            are: counter-clockwise "CCW", and clockwise "CW".

    """
    if repeat_first:
        n_points -= 1

    # Generate points about an ellipse with random eccentricity
    x, y = xy
    alpha = np.linspace(0, 2 * np.pi - (2 * np.pi / n_points), n_points)
    rx = radius * (RNG.random() + 0.5)
    ry = RNG.uniform(*eccentricity) * radius - 0.5 * rx
    x = rx * np.cos(alpha) + x + (RNG.random(n_points) - 0.5) * noise
    y = ry * np.sin(alpha) + y + (RNG.random(n_points) - 0.5) * noise
    boundary_coords = np.stack([x, y], axis=1).tolist()

    # Copy first coordinate to the end if required
    if repeat_first:
        boundary_coords = [*boundary_coords, boundary_coords[0]]

    # Swap direction
    if direction.strip().lower() == "cw":
        boundary_coords = boundary_coords[::-1]

    polygon = Polygon(boundary_coords)

    # Add random rotation
    angle = RNG.random() * 360
    return affinity.rotate(polygon, angle, origin="centroid")


def sample_where_1(props: dict[str, object]) -> bool:
    """Simple example predicate function for tests.

    Checks for a class = 1.

    """
    return props.get("class") == 1


def sample_where_123(props: dict[str, object]) -> bool:
    """Simple example predicate function for tests.

    Checks for a class = 123.

    """
    return props.get("class") == 123


def sample_select(props: dict[str, object]) -> tuple[object]:
    """Simple example select expression for tests.

    Gets the class value.

    """
    return props.get("class")


def sample_multi_select(props: dict[str, object]) -> tuple[object]:
    """Simple example select expression for tests.

    Gets the class value and the class mod 2.

    """
    return (props.get("class"), props.get("class") % 2)


def annotations_center_of_mass(annotations: list[Annotation]) -> Point:
    """Compute the mean of the annotation centroids."""
    centroids = [annotation.geometry.centroid for annotation in annotations]
    return MultiPoint(centroids).centroid


def test_annotation_repr() -> None:
    """Test the repr of an annotation."""
    annotation = Annotation(Polygon([(0, 0), (1, 1), (2, 0)]))
    assert isinstance(repr(annotation), str)
    assert repr(annotation).startswith("Annotation(")
    assert "POLYGON" in repr(annotation)
    assert repr(annotation).endswith(")")


# ----------------------------------------------------------------------
# Fixtures
# ----------------------------------------------------------------------


@pytest.fixture(scope="session")
def cell_grid() -> list[Polygon]:
    """Generate a grid of fake cell boundary polygon annotations."""
    return [cell_polygon((i * 25, j * 25)) for i, j in np.ndindex(*GRID_SIZE)]


@pytest.fixture(scope="session")
def points_grid() -> list[Polygon]:
    """Generate a grid of fake point annotations."""
    return [Point((i * 25, j * 25)) for i, j in np.ndindex(*GRID_SIZE)]


@pytest.fixture(scope="session")
def sample_triangle() -> Polygon:
    """Simple triangle polygon used for testing."""
    return Polygon([(0, 0), (1, 1), (2, 0)])


@pytest.fixture
def fill_store(
    cell_grid: list[Polygon],
    points_grid: list[Point],
) -> Callable[[list[str]], AnnotationStore]:
    """Factory fixture to fill stores with test data."""

    def _fill_store(
        store_class: AnnotationStore,
        path: str | Path,
    ) -> tuple[list[str], AnnotationStore]:
        """Private function to fill stores with data."""
        rng = np.random.default_rng()
        store = store_class(path)
        annotations = [Annotation(cell) for cell in cell_grid] + [
            Annotation(point, properties={"class": int(rng.integers(0, 5))})
            for point in points_grid
        ]
        keys = store.append_many(annotations)
        return keys, store

    return _fill_store


# ----------------------------------------------------------------------
# Annotation Tests
# ----------------------------------------------------------------------


def test_annotation_init_both_shapely_wkb() -> None:
    """Init annotation with both wkb and geometry."""
    with pytest.raises(ValueError, match="geometry and wkb"):
        _ = Annotation(geometry=Point(0, 0), wkb=Point(0, 0).wkb)


def test_annotation_init_neither_shapely_wkb() -> None:
    """Init annotation with neither wkb nor geometry."""
    with pytest.raises(ValueError, match="geometry or wkb"):
        _ = Annotation()


def test_polygon_annotation_from_wkb() -> None:
    """Test creating a polygon annotation from wkb."""
    coords = [[0, 0], [1, 1], [2, 0]]
    wkb = Polygon(coords).wkb
    ann = Annotation(wkb=wkb)
    assert ann.geometry == shapely.from_wkb(wkb)
    assert ann.properties == {}
    assert ann.geometry.type == str(GeometryType.POLYGON)


def test_polygon_annotation_from_shapely() -> None:
    """Test creating an annotation from shapely polygon then accessing coords."""
    polygon = Polygon([[0, 0], [1, 1], [2, 0]])
    ann = Annotation(geometry=polygon)
    assert ann.geometry == polygon
    assert ann.properties == {}
    assert ann.geometry.type == str(GeometryType.POLYGON)


def test_annotation_lazy_geometry() -> None:
    """Test that the geometry is not created until it is accessed."""
    ann = Annotation(wkb=Polygon([[0, 0], [1, 1], [2, 0]]).wkb)
    assert ann._wkb is not None
    assert ann._geometry is None
    _ = ann.geometry
    assert ann._geometry is not None


def test_lazy_geometry_type() -> None:
    """Test that getting geometry type from WKB does not create geometry."""
    ann = Annotation(wkb=Polygon([[0, 0], [1, 1], [2, 0]]).wkb)
    assert ann.geometry.type == str(GeometryType.POLYGON)
    assert ann._geometry is not None


def test_annotation_lazy_to_wkb() -> None:
    """Test that the geometry is not created until it is accessed."""
    polygon = Polygon([[0, 0], [1, 1], [2, 0]])
    ann = Annotation(wkb=polygon.wkb)
    _ = ann.to_wkb()
    assert ann._geometry is None


def test_annotation_lazy_wkb() -> None:
    """Test that the geometry is not created by accessing WKB."""
    polygon = Polygon([[0, 0], [1, 1], [2, 0]])
    ann = Annotation(wkb=polygon.wkb)
    _ = ann.wkb
    assert ann._geometry is None


def test_annotation_to_wkb_equals_wkb() -> None:
    """Test that to_wkb() and wkb are equal."""
    polygon = Polygon([[0, 0], [1, 1], [2, 0]])
    ann = Annotation(wkb=polygon.wkb)
    assert ann.to_wkb() == ann.wkb


def test_annotation_point_wkb_coords() -> None:
    """Test generating coordinates from WKB for Point.

    This should produce coordinates without generating a Shapely
    geometry.
    """
    point = Point([1, 2])
    ann = Annotation(wkb=point.wkb)
    coords = ann.coords
    assert ann._geometry is None
    assert isinstance(coords, np.ndarray)
    assert len(coords) == 1
    assert len(coords.shape) == 2
    # Check that coords are the same after creating geometry
    _ = ann.geometry
    assert ann._geometry is not None
    geom_coords = ann.coords
    assert np.array_equal(geom_coords, coords)


def test_annotation_polygon_wkb_coords() -> None:
    """Test generating coordinates from WKB for Polygon.

    This should produce coordinates without generating a Shapely
    geometry.
    """
    polygon = Polygon([[0, 0], [1, 1], [2, 0]])
    ann = Annotation(wkb=polygon.wkb)
    coords = ann.coords
    assert isinstance(coords, list)
    assert isinstance(coords[0], np.ndarray)
    assert ann._geometry is None
    assert len(coords[0].shape) == 2
    # Check that coords are the same after creating geometry
    _ = ann.geometry
    assert ann._geometry is not None
    geom_coords = ann.coords
    assert np.array_equal(geom_coords, coords)


def test_annotation_line_string_wkb_coords() -> None:
    """Test generating coordinates from WKB for LineString.

    This should produce coordinates without generating a Shapely
    geometry.
    """
    line = LineString([[0, 0], [1, 1], [2, 0]])
    ann = Annotation(wkb=line.wkb)
    coords = ann.coords
    assert isinstance(coords, np.ndarray)
    assert ann._geometry is None
    assert len(coords.shape) == 2
    # Check that coords are the same after creating geometry
    _ = ann.geometry
    assert ann._geometry is not None
    geom_coords = ann.coords
    assert np.array_equal(geom_coords, coords)


def test_annotation_multi_point_wkb_coords() -> None:
    """Test generating coordinates from WKB for MultiPoint.

    This should produce coordinates without generating a Shapely
    geometry.
    """
    multi_point = MultiPoint(
        [
            Point(0, 1),
            Point(2, 3),
        ],
    )
    ann = Annotation(wkb=multi_point.wkb)
    coords = ann.coords
    assert len(coords) == len(multi_point.geoms)
    assert isinstance(coords[0], np.ndarray)
    assert ann._geometry is None
    # Check that coords are the same after creating geometry
    _ = ann.geometry
    assert ann._geometry is not None
    geom_coords = ann.coords
    assert np.array_equal(geom_coords, coords)


def test_annotation_multi_polygon_wkb_coords() -> None:
    """Test generating coordinates from WKB for MultiPolygon.

    This should produce coordinates without generating a Shapely
    geometry.
    """
    multi_poly = MultiPolygon(
        polygons=[
            Polygon([[0, 0], [1, 1], [2, 0]]),
            Polygon([[0, 0], [1, 1], [2, 2], [3, 3]]),
        ],
    )
    ann = Annotation(wkb=multi_poly.wkb)
    coords = ann.coords
    assert len(coords) == len(multi_poly.geoms)
    assert isinstance(coords[0], list)
    assert ann._geometry is None
    # Check that coords are the same after creating geometry
    _ = ann.geometry
    assert ann._geometry is not None
    geom_coords = ann.coords
    assert all(np.array_equal(a, b) for a, b in zip_longest(geom_coords, coords))


def test_annotation_multi_line_string_wkb_coords() -> None:
    """Test generating coordinates from WKB for MultiLineString.

    This should produce coordinates without generating a Shapely
    geometry.
    """
    multi_line_string = MultiLineString(
        [
            LineString([(0, 0), (1, 1)]),
            LineString([(2, 2), (3, 3)]),
        ],
    )
    ann = Annotation(wkb=multi_line_string.wkb)
    coords = ann.coords
    assert len(coords) == len(multi_line_string.geoms)
    assert isinstance(coords[0], np.ndarray)
    assert ann._geometry is None
    # Check that coords are the same after creating geometry
    _ = ann.geometry
    assert ann._geometry is not None
    geom_coords = ann.coords
    assert all(np.array_equal(a, b) for a, b in zip_longest(geom_coords, coords))


def test_annotation_coords_wkb_unknown_geometry() -> None:
    """Test generating coordinates from WKB for unknown geometry type."""
    ann = Annotation(wkb=b"\x00\x07\x00\x00\x00")
    with pytest.raises(ValueError, match="Unknown geometry type"):
        _ = ann.coords


def test_annotation_coords_geometry_unknown_geometry() -> None:
    """Test generating coordinates from geometry for unknown geometry type."""
    ann = Annotation(geometry=GeometryCollection([Point(1, 2)]))
    with pytest.raises(ValueError, match="Unknown geometry type"):
        _ = ann.coords


def test_annotation_geometry_wkb() -> None:
    """Test generating WKB from geometry."""
    polygon = Polygon([[0, 0], [1, 1], [2, 0]])
    ann = Annotation(geometry=polygon)
    assert ann.wkb == polygon.wkb


def test_annotation_geometry_geometry_type() -> None:
    """Test getting GeometryType from Shapely geometry."""
    polygon = Polygon([[0, 0], [1, 1], [2, 0]])
    ann = Annotation(geometry=polygon)
    assert ann.geometry_type == GeometryType.POLYGON


def test_annotation_hash() -> None:
    """Test that the hash is the same for two annotations with the same geometry."""
    ann_1 = Annotation(Polygon([[0, 0], [1, 1], [2, 0]]))
    ann2 = Annotation(Polygon([[0, 0], [1, 1], [2, 0]]))
    assert hash(ann_1) == hash(ann2)


def test_annotation_eq_false() -> None:
    """Test that two annotations with different geometries are not equal."""
    ann_1 = Annotation(Polygon([[0, 0], [1, 1], [2, 0]]))
    ann_2 = Annotation(Polygon([[0, 0], [1, 1], [2, 0], [2, 2]]))
    assert ann_1 != ann_2


def test_annotation_eq_type_mismatch() -> None:
    """Test equality with another type."""
    ann_1 = Annotation(Polygon([[0, 0], [1, 1], [2, 0]]))
    assert ann_1 != "ann_2"


def test_annotation_wkt() -> None:
    """Test that Annotatoin.to_wkt() generates a valid WKT string."""
    ann = Annotation(Polygon([[0, 0], [1, 1], [2, 0]]))
    assert isinstance(ann.to_wkt(), str)
    assert ann.to_wkt().startswith("POLYGON")
    assert shapely.wkt.loads(ann.to_wkt()) == ann.geometry


def test_annotation_decode_unknown_wkb() -> None:
    """Test decoding an unknown WKB type."""
    wkb = b"\x01\x08\x00\x00\x00"
    with pytest.raises(ValueError, match="Unknown"):
        _ = Annotation.decode_wkb(wkb, 7)


# ----------------------------------------------------------------------
# Class-Specific Tests
# ----------------------------------------------------------------------


def test_sqlite_store_compile_options() -> None:
    """Test SQLiteStore compile options."""
    options = SQLiteStore.compile_options()
    assert all(isinstance(x, str) for x in options)


def test_sqlite_store_compile_options_exception(monkeypatch: object) -> None:
    """Test SQLiteStore compile options for exceptions."""
    monkeypatch.setattr(sqlite3, "sqlite_version_info", (3, 37, 0))
    monkeypatch.setattr(
        SQLiteStore,
        "compile_options",
        lambda _x: ["ENABLE_RTREE", "ENABLE_JSON1"],
        raising=True,
    )
    SQLiteStore()
    monkeypatch.setattr(SQLiteStore, "compile_options", lambda _x: [], raising=True)
    with pytest.raises(EnvironmentError, match="RTREE and JSON1"):
        SQLiteStore()


def test_sqlite_store_compile_options_exception_json_rtree(monkeypatch: object) -> None:
    """Test SQLiteStore compile options for exceptions."""
    monkeypatch.setattr(sqlite3, "sqlite_version_info", (3, 38, 0))
    monkeypatch.setattr(
        SQLiteStore,
        "compile_options",
        lambda _x: ["ENABLE_RTREE"],
        raising=True,
    )
    SQLiteStore()
    monkeypatch.setattr(SQLiteStore, "compile_options", lambda _x: [], raising=True)
    with pytest.raises(EnvironmentError, match="RTREE sqlite3"):
        SQLiteStore()


def test_sqlite_store_compile_options_exception_v3_38(monkeypatch: object) -> None:
    """Test SQLiteStore compile options for exceptions."""
    monkeypatch.setattr(sqlite3, "sqlite_version_info", (3, 38, 0))
    monkeypatch.setattr(
        SQLiteStore,
        "compile_options",
        lambda _x: ["OMIT_JSON"],
        raising=True,
    )
    with pytest.raises(EnvironmentError, match="JSON must not"):
        SQLiteStore()


def test_sqlite_store_compile_options_missing_math(
    monkeypatch: object,
    caplog: pytest.LogCaptureFixture,
) -> None:
    """Test that a warning is shown if the sqlite math module is missing."""
    # Reset filters in logger.
    for filter_ in logger.filters[:]:
        logger.removeFilter(filter_)
    monkeypatch.setattr(
        SQLiteStore,
        "compile_options",
        lambda _x: ["ENABLE_JSON1", "ENABLE_RTREE"],
        raising=True,
    )
    SQLiteStore()
    assert "SQLite math functions are not enabled" in caplog.text


def test_sqlite_store_multiple_connection(tmp_path: Path) -> None:
    """Test SQLiteStore multiple connections."""
    store = SQLiteStore(tmp_path / "annotations.db")
    store2 = SQLiteStore(tmp_path / "annotations.db")
    assert len(store) == len(store2)


def test_sqlite_store_index_type_error() -> None:
    """Test adding an index of invalid type."""
    store = SQLiteStore()
    with pytest.raises(TypeError, match="where"):
        store.create_index("foo", lambda _g, p: "foo" in p)


def test_sqlite_store_index_version_error(monkeypatch: object) -> None:
    """Test adding an index with SQlite <3.9."""
    store = SQLiteStore()
    monkeypatch.setattr(sqlite3, "sqlite_version_info", (3, 8, 0))
    with pytest.raises(EnvironmentError, match="Requires sqlite version 3.9.0"):
        store.create_index("foo", lambda _, p: "foo" in p)


def test_sqlite_store_index_str(fill_store: Callable, tmp_path: Path) -> None:
    """Test that adding an index improves performance."""
    _, store = fill_store(SQLiteStore, tmp_path / "polygon.db")

    def query() -> list[int]:
        """Test query."""
        return store.iquery((0, 0, 1e4, 1e4), where="props['class'] == 0")

    def alt_query() -> list[int]:
        """Alternative query to avoid temporary caches giving unfair advantage."""
        return store.iquery((0, 0, 1e4, 1e4), where="has_key(props, 'foo')")

    # Do an initial bunch of queries to initialise any internal state or
    # caches.
    _ = timeit(query, number=10)
    # Time query without index
    t1 = timeit(query, number=50)
    # Create the index
    properties_predicate = "props['class']"
    store.create_index("test_index", properties_predicate)
    # Do another unrelated query
    _ = timeit(alt_query, number=10)
    # Time the original query with the index
    t2 = timeit(query, number=50)
    assert t2 < t1


def test_sqlite_create_index_no_analyze(fill_store: Callable, tmp_path: Path) -> None:
    """Test that creating an index without ANALYZE."""
    _, store = fill_store(SQLiteStore, tmp_path / "polygon.db")
    properties_predicate = "props['class']"
    store.create_index("test_index", properties_predicate, analyze=False)
    assert "test_index" in store.indexes()


def test_sqlite_pquery_warn_no_index(
    fill_store: Callable,
    caplog: pytest.LogCaptureFixture,
) -> None:
    """Test that querying without an index warns."""
    _, store = fill_store(SQLiteStore, ":memory:")
    store.pquery("*", unique=False)
    assert "Query is not using an index." in caplog.text


def test_sqlite_pquery_nowarn_index(
    fill_store: Callable,
    caplog: pytest.LogCaptureFixture,
) -> None:
    """Test that after making index, does not warn."""
    _, store = fill_store(SQLiteStore, ":memory:")
    store.create_index("test_index", "props['class']")
    store.pquery("props['class']")
    assert "Query is not using an index." not in caplog.text


def test_sqlite_store_indexes(fill_store: Callable, tmp_path: Path) -> None:
    """Test getting a list of index names."""
    _, store = fill_store(SQLiteStore, tmp_path / "polygon.db")
    store.create_index("test_index", "props['class']")
    assert "test_index" in store.indexes()


def test_sqlite_drop_index_error(fill_store: Callable, tmp_path: Path) -> None:
    """Test dropping an index that does not exist."""
    _, store = fill_store(SQLiteStore, tmp_path / "polygon.db")
    with pytest.raises(sqlite3.OperationalError, match="no such index"):
        store.drop_index("test_index")


def test_sqlite_store_unsupported_compression(sample_triangle: Polygon) -> None:
    """Test that using an unsupported compression str raises error."""
    store = SQLiteStore(compression="foo")
    with pytest.raises(ValueError, match="Unsupported"):
        _ = store.serialise_geometry(sample_triangle)


def test_sqlite_optimize(fill_store: Callable, tmp_path: Path) -> None:
    """Test optimizing the database."""
    _, store = fill_store(SQLiteStore, tmp_path / "polygon.db")
    store.optimize()


def test_sqlite_store_no_compression(sample_triangle: Polygon) -> None:
    """Test that using no compression raises no error."""
    store = SQLiteStore(compression=None)
    serialised = store.serialise_geometry(sample_triangle)
    deserialised = store.deserialize_geometry(serialised)
    assert deserialised.wkb == sample_triangle.wkb


def test_sqlite_store_unsupported_decompression() -> None:
    """Test that using an unsupported decompression str raises error."""
    store = SQLiteStore(compression="foo")
    with pytest.raises(ValueError, match="Unsupported"):
        _ = store.deserialize_geometry(b"")


def test_sqlite_store_wkt_deserialisation(sample_triangle: Polygon) -> None:
    """Test WKT deserialisation."""
    store = SQLiteStore(compression=None)
    wkt = sample_triangle.wkt
    geom = store.deserialize_geometry(wkt)
    assert geom == sample_triangle


def test_sqlite_store_wkb_deserialisation(sample_triangle: Polygon) -> None:
    """Test WKB deserialisation.

    Test the default stattic method in the ABC.

    """
    wkb = sample_triangle.wkb
    geom = AnnotationStore.deserialize_geometry(wkb)
    assert geom == sample_triangle


def test_sqlite_store_metadata_get_key() -> None:
    """Test getting a metadata entry."""
    store = SQLiteStore()
    assert store.metadata["compression"] == "zlib"


def test_sqlite_store_metadata_get_keyerror() -> None:
    """Test getting a metadata entry that does not exists."""
    store = SQLiteStore()
    with pytest.raises(KeyError):
        store.metadata["foo"]


def test_sqlite_store_metadata_delete_keyerror() -> None:
    """Test deleting a metadata entry that does not exists."""
    store = SQLiteStore(compression=None)
    with pytest.raises(KeyError):
        del store.metadata["foo"]


def test_sqlite_store_metadata_delete() -> None:
    """Test adding and deleting a metadata entry."""
    store = SQLiteStore(compression=None)
    store.metadata["foo"] = 1
    assert "foo" in store.metadata
    del store.metadata["foo"]
    assert "foo" not in store.metadata


def test_sqlite_store_metadata_iter() -> None:
    """Test iterating over metadata entries."""
    conn = sqlite3.Connection(":memory:")
    metadata = SQLiteMetadata(conn)
    metadata["foo"] = 1
    metadata["bar"] = 2
    assert set(metadata.keys()) == {"foo", "bar"}


def test_sqlite_store_metadata_len() -> None:
    """Test len of metadata entries."""
    conn = sqlite3.Connection(":memory:")
    metadata = SQLiteMetadata(conn)
    metadata["foo"] = 1
    metadata["bar"] = 2
    assert len(metadata) == 2


def test_sqlite_drop_index() -> None:
    """Test creating and dropping an index."""
    store = SQLiteStore()
    store.create_index("foo", "props['class']")
    assert "foo" in store.indexes()
    store.drop_index("foo")
    assert "foo" not in store.indexes()


def test_sqlite_drop_index_fail() -> None:
    """Test dropping an index that does not exist."""
    store = SQLiteStore()
    with pytest.raises(sqlite3.OperationalError):
        store.drop_index("foo")


def test_sqlite_optimize_no_vacuum(fill_store: Callable, tmp_path: Path) -> None:
    """Test running the optimize function on an SQLiteStore without VACUUM."""
    _, store = fill_store(SQLiteStore, tmp_path / "polygon.db")
    store.optimize(limit=0, vacuum=False)


def test_sqlite_wkb(fill_store: Callable) -> None:
    """Test that SQLiteStore returns annotations with WKB geometry."""
    _, store = fill_store(SQLiteStore, ":memory:")
    results = store.query((0, 0, 30, 30))
    assert len(results) == 8
    assert all(annotation._wkb is not None for annotation in results.values())


def test_annotation_to_geojson() -> None:
    """Test converting an annotation to geojson."""
    annotation = Annotation(
        geometry=Point(0, 0),
        properties={"foo": "bar", "baz": "qux"},
    )
    geojson = json.loads(annotation.to_geojson())
    assert geojson["type"] == "Feature"
    assert geojson["geometry"]["type"] == "Point"
    assert geojson["properties"] == {"foo": "bar", "baz": "qux"}


def test_remove_area_column(fill_store: Callable) -> None:
    """Test removing an area column."""
    _, store = fill_store(SQLiteStore, ":memory:")
    store.remove_area_column()
    assert "area" not in store._get_table_columns()
    result = store.query((0, 0, 1000, 1000))
    assert len(result) == 200

    store.add_area_column()
    assert "area" in store.indexes()
    store.remove_area_column()
    # Check that the index is removed if its there
    assert "area" not in store.indexes()


def test_remove_area_column_indexed(fill_store: Callable) -> None:
    """Test removing an area column if there's an index on it."""
    _, store = fill_store(SQLiteStore, ":memory:")
    store.create_index("area", '"area"')
    store.remove_area_column()
    assert "area" not in store._get_table_columns()
    result = store.query((0, 0, 1000, 1000))
    assert len(result) == 200


def test_add_area_column(fill_store: Callable) -> None:
    """Test adding an area column."""
    _, store = fill_store(SQLiteStore, ":memory:")
    store.remove_area_column()
    store.add_area_column()
    assert "area" in store.indexes()
    assert "area" in store._get_table_columns()

    # check the results are properly sorted by area
    result = store.query((0, 0, 100, 100))
    areas = [ann.geometry.area for ann in result.values()]
    assert areas == sorted(areas, reverse=True)

    # check add index option of add_area_column
    _, store = fill_store(SQLiteStore, ":memory:")
    store.remove_area_column()
    assert "area" not in store.indexes()
    store.add_area_column(mk_index=False)
    assert "area" not in store.indexes()


def test_query_min_area_no_area_column(fill_store: Callable) -> None:
    """Test querying with a minimum area when there is no area column."""
    _, store = fill_store(SQLiteStore, ":memory:")
    store.remove_area_column()
    with pytest.raises(ValueError, match="without an area column"):
        store.query((0, 0, 1000, 1000), min_area=1)


def test_auto_commit(fill_store: Callable, tmp_path: Path) -> None:
    """Test auto commit.

    Check that if auto-commit is False, the changes are not committed until
    commit() is called.

    """
    _, store = fill_store(SQLiteStore, tmp_path / "polygon.db")
    store.close()
    store = SQLiteStore(tmp_path / "polygon.db", auto_commit=False)
    keys = list(store.keys())
    store.patch(keys[0], Point(-500, -500))
    store.append_many([Annotation(Point(10, 10), {}), Annotation(Point(20, 20), {})])
    store.remove_many(keys[5:10])
    store.clear()
    store.close()
    store = SQLiteStore(tmp_path / "polygon.db")
    result = store.query((0, 0, 1000, 1000))
    assert len(result) == 200  # check none of the changes were committed
    store = SQLiteStore(tmp_path / "polygon2.db", auto_commit=False)
    store.append_many([Annotation(Point(10, 10), {}), Annotation(Point(20, 20), {})])
    store.commit()
    store.close()
    store = SQLiteStore(tmp_path / "polygon2.db")
    assert len(store) == 2  # check explicitly committing works


def test_init_base_class_exception() -> None:
    """Test that the base class cannot be initialized."""
    with pytest.raises(TypeError, match="abstract class"):
        AnnotationStore()  # skipcq: PYL-E0110


# ----------------------------------------------------------------------
# Annotation Store Interface Tests (AnnotationStoreABC)
# ----------------------------------------------------------------------


class TestStore:
    """Define TestStore to test AnnotationStore for multiple scenarios."""

    scenarios: ClassVar[list[tuple[str, dict]]] = [
        ("Dictionary", {"store_cls": DictionaryStore}),
        ("SQLite", {"store_cls": SQLiteStore}),
    ]

    @staticmethod
    def test_open_close(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test opening and closing a store."""
        path = tmp_path / "polygons"
        keys, store = fill_store(store_cls, path)
        store.close()
        store2 = store.open(path)
        assert len(store2) == len(keys)

    @staticmethod
    def test_append_many(
        cell_grid: list[Polygon],
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk append of annotations."""
        rng = np.random.default_rng()
        store = store_cls(tmp_path / "polygons")
        annotations = [
            Annotation(cell, {"class": int(rng.integers(0, 7))}) for cell in cell_grid
        ]
        keys = store.append_many(annotations)
        assert len(keys) == len(cell_grid)

    @staticmethod
    def test_append_many_with_keys(
        cell_grid: list[Polygon],
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk append of annotations with keys."""
        rng = np.random.default_rng()
        store = store_cls(tmp_path / "polygons")
        annotations = [
            Annotation(cell, {"class": int(rng.integers(0, 7))}) for cell in cell_grid
        ]
        keys = [chr(n) for n, _ in enumerate(annotations)]
        returned_keys = store.append_many(annotations, keys=keys)
        assert len(returned_keys) == len(cell_grid)
        assert keys == returned_keys

    @staticmethod
    def test_append_many_with_keys_len_mismatch(
        cell_grid: list[Polygon],
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk append of annotations with keys of wrong length."""
        rng = np.random.default_rng()
        store = store_cls(tmp_path / "polygons")
        annotations = [
            Annotation(cell, {"class": int(rng.integers(0, 7))}) for cell in cell_grid
        ]
        keys = ["foo"]
        with pytest.raises(ValueError, match="equal"):
            store.append_many(annotations, keys=keys)

    @staticmethod
    def test_query_bbox(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test query with a bounding box."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        results = store.query((0, 0, 25, 25))
        assert len(results) == 8

    @staticmethod
    def test_iquery_bbox(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test iquery with a bounding box."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        results = store.iquery((0, 0, 25, 25))
        assert len(results) == 8
        assert all(isinstance(key, str) for key in results)

    @staticmethod
    def test_query_polygon(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test query with a non-rectangular geometry."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        results = store.query(Polygon([(0, 0), (0, 25), (1, 1), (25, 0)]))
        assert len(results) == 6
        assert all(isinstance(ann, Annotation) for ann in results.values())

    @staticmethod
    def test_iquery_polygon(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test iquery with a non-rectangular geometry."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        results = store.iquery(Polygon([(0, 0), (0, 25), (1, 1), (25, 0)]))
        assert len(results) == 6
        assert all(isinstance(key, str) for key in results)

    @staticmethod
    def test_patch(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test patching an annotation."""
        keys, store = fill_store(
            store_cls,
            tmp_path / "polygon.db",
        )
        key = keys[0]
        new_geometry = Polygon([(0, 0), (1, 1), (2, 2)])
        # Geometry update
        store.patch(key, new_geometry)
        assert store[key].geometry == new_geometry
        # Properties update
        store.patch(key, properties={"abc": 123})
        assert store[key].properties["abc"] == 123

    @staticmethod
    def test_patch_append(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test patching an annotation that does not exist."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        new_geometry = Polygon([(0, 0), (1, 1), (2, 2)])
        store.patch("foo", new_geometry)
        assert store["foo"].geometry == new_geometry

    @staticmethod
    def test_patch_many(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk patch."""
        keys, store = fill_store(
            store_cls,
            tmp_path / "polygon.db",
        )
        new_geometry = Polygon([(0, 0), (1, 1), (2, 2)])
        store.patch_many(
            keys,
            repeat(new_geometry, len(keys)),
            repeat({"abc": 123}, len(keys)),
        )

        for _, key in enumerate(keys[:10]):
            assert store[key].geometry == new_geometry
            assert store[key].properties["abc"] == 123

    @staticmethod
    def test_patch_many_no_properies(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk patch with no properties."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        new_geometry = Polygon([(0, 0), (1, 1), (2, 2)])
        store.patch_many(keys, repeat(new_geometry, len(keys)))

        for _, key in enumerate(keys[:10]):
            assert store[key].geometry == new_geometry
            assert store[key].properties == {}

    @staticmethod
    def test_patch_many_no_geometry(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk patch with no geometry."""
        keys, store = fill_store(
            store_cls,
            tmp_path / "polygon.db",
        )
        store.patch_many(keys, properties_iter=repeat({"abc": 123}, len(keys)))

        for _, key in enumerate(keys[:10]):
            assert store[key].geometry is not None
            assert store[key].properties["abc"] == 123

    @staticmethod
    def test_patch_many_no_geometry_no_properties(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk patch with no geometry and no properties."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        with pytest.raises(ValueError, match="At least one"):
            store.patch_many(keys)

    @staticmethod
    def test_patch_many_append(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk patching annotations that do not exist."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        new_geometry = Polygon([(0, 0), (1, 1), (2, 2)])
        store.patch_many(["foo", "bar"], repeat(new_geometry, 2))
        assert store["foo"].geometry == new_geometry
        assert store["bar"].geometry == new_geometry

    @staticmethod
    def test_patch_many_len_mismatch(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk patch with wrong number of keys."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        new_geometry = Polygon([(0, 0), (1, 1), (2, 2)])
        with pytest.raises(ValueError, match="equal"):
            store.patch_many(keys[1:], repeat(new_geometry, 10))

    @staticmethod
    def test_keys(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test getting a keys iterator."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        keys = list(keys)
        assert len(list(store.keys())) == len(keys)
        assert isinstance(next(iter(store.keys())), type(keys[0]))

    @staticmethod
    def test_remove(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test removing an annotation."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        key = keys[0]
        store.remove(key)
        assert len(store) == FILLED_LEN - 1

    @staticmethod
    def test_delitem(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test using the delitem syntax."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        key = keys[0]
        del store[key]
        assert len(store) == FILLED_LEN - 1

    @staticmethod
    def test_remove_many(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test bulk deletion."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        store.remove_many(keys)
        assert len(store) == 0

    @staticmethod
    def test_len(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test finding the number of annotation via the len operator."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        assert len(store) == FILLED_LEN

    @staticmethod
    def test_contains(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test using the contains (in) operator."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        for key in keys:
            assert key in store

    @staticmethod
    def test_iter(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test iterating over the store."""
        keys, store = fill_store(store_cls, tmp_path / "polygon.db")
        for key in store:
            assert key in keys

    @staticmethod
    def test_getitem(
        fill_store: Callable,
        tmp_path: Path,
        sample_triangle: Polygon,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test the getitem syntax."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        key = store.append(Annotation(sample_triangle))
        annotation = store[key]
        assert annotation.geometry == sample_triangle
        assert annotation.properties == {}

    @staticmethod
    def test_setitem(
        fill_store: Callable,
        tmp_path: Path,
        sample_triangle: Polygon,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test the setitem syntax."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        key = store.append(Annotation(sample_triangle))
        new_geometry = Polygon([(0, 0), (1, 1), (2, 2)])
        new_properties = {"abc": 123}
        store[key] = Annotation(new_geometry, new_properties)
        assert store[key] == Annotation(new_geometry, new_properties)

    @staticmethod
    def test_getitem_setitem_cycle(
        fill_store: Callable,
        tmp_path: Path,
        sample_triangle: Polygon,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test getting an setting an annotation."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        key = store.append(Annotation(sample_triangle, {"class": 0}))
        annotation = store[key]
        store[key] = annotation
        assert store[key] == annotation

    @staticmethod
    def test_from_dataframe(
        cell_grid: list[Polygon],
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test loading from to a pandas dataframe."""
        cell_grid_df = pd.DataFrame.from_records(
            [
                {
                    "geometry": cell,
                    "row_id": n,
                }
                for n, cell in enumerate(cell_grid)
            ],
        )
        store = store_cls.from_dataframe(cell_grid_df)
        keys = list(store.keys())
        annotation = store[keys[0]]
        assert "row_id" in annotation.properties

    @staticmethod
    def test_to_dataframe(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test converting to a pandas dataframe."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        store_as_df = store.to_dataframe()
        assert isinstance(store_as_df, pd.DataFrame)
        assert len(store_as_df) == FILLED_LEN
        assert "geometry" in store_as_df.columns
        assert store_as_df.index.name == "key"
        assert isinstance(store_as_df.geometry.iloc[0], Polygon)

    @staticmethod
    def test_features(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test converting to a features dictionaries."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        features = store.features()
        assert isinstance(features, Generator)
        features = list(features)
        assert len(features) == FILLED_LEN
        assert isinstance(features[0], dict)
        assert all(
            {"type", "geometry", "properties"} == set(f.keys()) for f in features
        )

    @staticmethod
    def test_to_geodict(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test converting to a geodict."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        geodict = store.to_geodict()
        assert isinstance(geodict, dict)
        assert "features" in geodict
        assert "type" in geodict
        assert geodict["type"] == "FeatureCollection"
        assert geodict["features"] == list(store.features())

    @staticmethod
    def test_from_geojson_str(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test loading from geojson with a file path string."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        geojson = store.to_geojson()
        store2 = store_cls.from_geojson(geojson)
        assert len(store) == len(store2)

    @staticmethod
    def test_from_geojson_file(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test loading from geojson with a file handle."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        store.to_geojson(tmp_path / "polygon.json")
        with Path.open(tmp_path / "polygon.json") as file_handle:
            store2 = store_cls.from_geojson(file_handle)
        assert len(store) == len(store2)

    @staticmethod
    def test_from_geojson_path(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test loading from geojson with a file path."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        store.to_geojson(tmp_path / "polygon.json")
        store2 = store_cls.from_geojson(tmp_path / "polygon.json")
        assert len(store) == len(store2)

    @staticmethod
    def test_from_geojson_path_transform(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test loading from geojson with a transform."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        com = annotations_center_of_mass(list(store.values()))
        store.to_geojson(tmp_path / "polygon.json")

        # load the store translated so that origin is (100,100) and scaled by 2
        def dummy_transform(annotation: Annotation) -> Annotation:
            return annotation

        store2 = store_cls.from_geojson(
            tmp_path / "polygon.json",
            scale_factor=(2, 2),
            origin=(100, 100),
            transform=dummy_transform,
        )
        assert len(store) == len(store2)
        com2 = annotations_center_of_mass(list(store2.values()))
        assert com2.x == pytest.approx((com.x - 100) * 2)
        assert com2.y == pytest.approx((com.y - 100) * 2)

    @staticmethod
    def test_transform(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test translating a store."""

        def test_translation(geom: Geometry) -> None:
            """Performs a translation of input geometry."""
            return affinity.translate(geom, 100, 100)

        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        com = annotations_center_of_mass(list(store.values()))
        store.transform(test_translation)
        com2 = annotations_center_of_mass(list(store.values()))
        assert com2.x - com.x == pytest.approx(100)
        assert com2.y - com.y == pytest.approx(100)

    @staticmethod
    def test_to_geojson_str(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test exporting to ndjson with a file path string."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        geojson = store.to_geojson()
        assert isinstance(geojson, str)
        geodict = json.loads(geojson)
        assert "features" in geodict
        assert "type" in geodict
        assert geodict["type"] == "FeatureCollection"
        assert len(geodict["features"]) == len(list(store.features()))

    @staticmethod
    def test_to_geojson_file(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test exporting to ndjson with a file handle."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        with Path.open(tmp_path / "polygon.json", "w") as fh:
            geojson = store.to_geojson(fp=fh)
        assert geojson is None
        with Path.open(tmp_path / "polygon.json") as fh:
            geodict = json.load(fh)
        assert "features" in geodict
        assert "type" in geodict
        assert geodict["type"] == "FeatureCollection"
        assert len(geodict["features"]) == len(list(store.features()))

    @staticmethod
    def test_to_geojson_path(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test exporting to geojson with a file path."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        geojson = store.to_geojson(fp=tmp_path / "polygon.json")
        assert geojson is None
        with Path.open(tmp_path / "polygon.json") as fh:
            geodict = json.load(fh)
        assert "features" in geodict
        assert "type" in geodict
        assert geodict["type"] == "FeatureCollection"
        assert len(geodict["features"]) == len(list(store.features()))

    @staticmethod
    def test_to_ndjson_str(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test exporting to ndjson with a file path string."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        ndjson = store.to_ndjson()
        for line in ndjson.split():
            assert isinstance(line, str)
            feature = json.loads(line)
            assert "type" in feature
            assert "geometry" in feature
            assert "properties" in feature

    @staticmethod
    def test_to_ndjson_file(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test exporting to ndjson with a file handle."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        with Path.open(tmp_path / "polygon.ndjson", "w") as fh:
            ndjson = store.to_ndjson(fp=fh)
        assert ndjson is None
        with Path.open(tmp_path / "polygon.ndjson") as fh:
            for line in fh.readlines():
                assert isinstance(line, str)
                feature = json.loads(line)
                assert "type" in feature
                assert "geometry" in feature
                assert "properties" in feature

    @staticmethod
    def test_to_ndjson_path(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test exporting to ndjson with a file path."""
        _, store = fill_store(store_cls, tmp_path / "polygon.db")
        ndjson = store.to_ndjson(fp=tmp_path / "polygon.ndjson")
        assert ndjson is None
        with Path.open(tmp_path / "polygon.ndjson") as fh:
            for line in fh.readlines():
                assert isinstance(line, str)
                feature = json.loads(line)
                assert "type" in feature
                assert "geometry" in feature
                assert "properties" in feature

    @staticmethod
    def test_dump(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test dumping to a file path."""
        _, store = fill_store(store_cls, ":memory:")
        store.dump(tmp_path / "dump_test.db")
        assert (tmp_path / "dump_test.db").stat().st_size > 0

    @staticmethod
    def test_dump_file_handle(
        fill_store: Callable,
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test dumping to a file handle."""
        _, store = fill_store(store_cls, ":memory:")
        with Path.open(tmp_path / "dump_test.db", "w") as fh:
            store.dump(fh)
        assert (tmp_path / "dump_test.db").stat().st_size > 0

    @staticmethod
    def test_dumps(fill_store: Callable, store_cls: type[AnnotationStore]) -> None:
        """Test dumping by returning a string."""
        _, store = fill_store(store_cls, ":memory:")
        string = store.dumps()
        assert isinstance(string, str)

    @staticmethod
    def test_iquery_predicate_str(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test iquering with a predicate string."""
        keys, store = fill_store(store_cls, ":memory:")
        store.patch(keys[0], properties={"class": 123})
        results = store.iquery((0, 0, 1024, 1024), where="props.get('class') == 123")
        assert len(results) == 1
        assert results[0] == keys[0]

    @staticmethod
    def test_iquery_predicate_callable(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test iquering with a predicate function."""
        keys, store = fill_store(store_cls, ":memory:")
        store.patch(keys[0], properties={"class": 123})
        results = store.iquery(
            (0, 0, 1024, 1024),
            where=lambda props: props.get("class") == 123,
        )
        assert len(results) == 1
        assert results[0] == keys[0]

    @staticmethod
    def test_iquery_predicate_pickle(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test iquering with a pickled predicate function."""
        keys, store = fill_store(store_cls, ":memory:")
        store.patch(keys[0], properties={"class": 123})

        results = store.query((0, 0, 1024, 1024), where=pickle.dumps(sample_where_123))
        assert len(results) == 1

    @staticmethod
    def test_query_predicate_str(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test quering with a predicate string."""
        keys, store = fill_store(store_cls, ":memory:")
        store.patch(keys[0], properties={"class": 123})
        results = store.query((0, 0, 1024, 1024), where="props.get('class') == 123")
        assert len(results) == 1

    @staticmethod
    def test_query_predicate_callable(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test quering with a predicate function."""
        keys, store = fill_store(store_cls, ":memory:")
        store.patch(keys[0], properties={"class": 123})
        results = store.query(
            # (0, 0, 1024, 1024),  # noqa: ERA001
            where=lambda props: props.get("class") == 123,
        )
        assert len(results) == 1

    @staticmethod
    def test_query_predicate_pickle(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test quering with a pickled predicate function."""
        keys, store = fill_store(store_cls, ":memory:")
        store.patch(keys[0], properties={"class": 123})

        results = store.query((0, 0, 1024, 1024), where=pickle.dumps(sample_where_123))
        assert len(results) == 1

    @staticmethod
    def test_append_invalid_geometry(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that appending invalid geometry raises an exception."""
        store = store_cls()
        with pytest.raises(TypeError, match="geometry"):
            store.append(Annotation("point", {}))

    @staticmethod
    def test_update_invalid_geometry(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that updating  a new key and None geometry raises an exception."""
        store = store_cls()
        key = "foo"
        with pytest.raises((TypeError, ValueError)):
            store.patch(key, geometry=None, properties={"class": 123})

    @staticmethod
    def test_pop_key(fill_store: Callable, store_cls: type[AnnotationStore]) -> None:
        """Test popping an annotation by key."""
        keys, store = fill_store(store_cls, ":memory:")
        assert keys[0] in store
        annotation = store.pop(keys[0])
        assert keys[0] not in store
        assert annotation not in store.values()

    @staticmethod
    def test_pop_key_error(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that popping a key that is not in the store raises an exception."""
        store = store_cls()
        with pytest.raises(KeyError):
            store.pop("foo")

    @staticmethod
    def test_popitem(fill_store: Callable, store_cls: type[AnnotationStore]) -> None:
        """Test popping a key and annotation by key."""
        keys, store = fill_store(store_cls, ":memory:")
        key, annotation = store.popitem()
        assert key in keys
        assert key not in store
        assert annotation not in store.values()

    @staticmethod
    def test_popitem_empty_error(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that popping an empty store raises an exception."""
        store = store_cls()
        with pytest.raises(KeyError):
            store.popitem()

    @staticmethod
    def test_setdefault(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
        sample_triangle: list[Polygon],
    ) -> None:
        """Test setting a default value for a key."""
        store = store_cls()
        default = Annotation(sample_triangle)
        assert "foo" not in store
        assert store.setdefault("foo", default) == default
        assert "foo" in store
        assert default in store.values()

    @staticmethod
    def test_setdefault_error(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
        sample_triangle: Polygon,  # noqa: ARG004
    ) -> None:
        """Test setting a default value for a key with invalid type."""
        store = store_cls()
        with pytest.raises(TypeError):
            store.setdefault("foo", {})

    @staticmethod
    def test_get(fill_store: Callable, store_cls: type[AnnotationStore]) -> None:
        """Test getting an annotation by key."""
        keys, store = fill_store(store_cls, ":memory:")
        assert keys[0] in store
        assert store.get(keys[0]) == store[keys[0]]

    @staticmethod
    def test_get_default(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test getting a default value for a key."""
        store = store_cls()
        assert "foo" not in store
        assert store.get("foo") is None

    @staticmethod
    def test_eq(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test comparing two stores for equality."""
        store1 = store_cls()
        store2 = store_cls()
        assert store1 == store2

        store1 = fill_store(store_cls, ":memory:")[1]
        assert store1 != store2

        for key, value in store1.items():
            store2[key] = value
        assert store1 == store2

    @staticmethod
    def test_ne(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test comparing two stores for inequality."""
        store1 = fill_store(store_cls, ":memory:")[1]
        store2 = fill_store(store_cls, ":memory:")[1]
        assert store1 != store2

    @staticmethod
    def test_clear(fill_store: Callable, store_cls: type[AnnotationStore]) -> None:
        """Test clearing a store."""
        keys, store = fill_store(store_cls, ":memory:")
        store.clear()
        assert keys[0] not in store
        assert len(store) == 0
        assert not store

    @staticmethod
    def test_update(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
        sample_triangle: Polygon,
    ) -> None:
        """Test updating a store with a dictionary."""
        _, store = fill_store(store_cls, ":memory:")
        annotations = {
            "foo": Annotation(sample_triangle),
        }
        assert "foo" not in store
        store.update(annotations)
        assert "foo" in store
        assert store["foo"] == annotations["foo"]

    @staticmethod
    def test_cast_dict(fill_store: Callable, store_cls: type[AnnotationStore]) -> None:
        """Test casting a store to a dictionary."""
        keys, store = fill_store(store_cls, ":memory:")
        store_dict = dict(store)
        assert keys[0] in store_dict
        assert store[keys[0]] in store_dict.values()

    @staticmethod
    def test_query_invalid_geometry_predicate(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that invalid geometry predicate raises an exception."""
        store = store_cls()
        with pytest.raises(ValueError, match="Invalid geometry predicate"):
            store.query((0, 0, 1024, 1024), geometry_predicate="foo")

    @staticmethod
    def test_query_no_geometry_or_where(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that query raises exception when no geometry or predicate given."""
        store = store_cls()
        with pytest.raises(ValueError, match="At least one of"):
            store.query()

    @staticmethod
    def test_iquery_invalid_geometry_predicate(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that invalid geometry predicate raises an exception."""
        store = store_cls()
        with pytest.raises(ValueError, match="Invalid geometry predicate"):
            store.iquery((0, 0, 1024, 1024), geometry_predicate="foo")

    @staticmethod
    def test_serialise_deseialise_geometry(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that geometry can be serialised and deserialised."""
        _, store = fill_store(store_cls, ":memory:")
        for annotation in store.values():
            geometry = annotation.geometry
            serialised = store.serialise_geometry(geometry)
            deserialised = store.deserialize_geometry(serialised)
            if isinstance(serialised, str):
                assert geometry.wkt == deserialised.wkt
            else:
                assert geometry.wkb == deserialised.wkb

    @staticmethod
    def test_commit(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
        tmp_path: Path,
    ) -> None:
        """Test committing a store."""
        store_path = tmp_path / "test_store"
        test_store = store_cls(store_path)
        test_store["foo"] = Annotation(Point(0, 0))
        test_store.commit()
        assert store_path.exists()
        test_store.close()
        del test_store  # skipcq: PTC-W0043
        test_store = store_cls(store_path)
        assert "foo" in test_store

    @staticmethod
    def test_load_cases_error(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that loading a store with an invalid file handle raises an exception."""
        store = store_cls()
        with pytest.raises(IOError, match="Invalid file handle or path"):
            store._load_cases(["foo"], lambda: None, lambda: None)

    @staticmethod
    def test_py39_init(
        fill_store: Callable,  # noqa: ARG004
        store_cls: type[AnnotationStore],
        monkeypatch: object,
    ) -> None:
        """Test that __init__ is compatible with Python 3.9."""
        py39_version = (3, 9, 0)

        class Connection(sqlite3.Connection):
            """Mock SQLite connection."""

            def create_function(
                self: Connection,
                name: str,
                num_params: int,
                func: object,  # noqa: ARG002
            ) -> None:
                """Mock create_function without `deterministic` kwarg."""
                return self.create_function(self, name, num_params)

        monkeypatch.setattr(sys, "version_info", py39_version)
        monkeypatch.setattr(sqlite3, "Connection", Connection)
        _ = store_cls()

    @staticmethod
    def test_bquery(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying a store with a bounding box."""
        _, store = fill_store(store_cls, ":memory:")
        dictionary = store.bquery((0, 0, 1e10, 1e10))
        assert isinstance(dictionary, dict)
        assert len(dictionary) == len(store)

    @staticmethod
    def test_bquery_polygon(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying a store with a polygon."""
        _, store = fill_store(store_cls, ":memory:")
        dictionary = store.bquery(Polygon.from_bounds(0, 0, 1e10, 1e10))
        assert isinstance(dictionary, dict)
        assert len(dictionary) == len(store)

    @staticmethod
    def test_bquery_callable(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying a store with a bounding box and a Callable where."""
        keys, store = fill_store(store_cls, ":memory:")
        store.patch(keys[0], properties={"class": 123})
        dictionary = store.bquery(
            (0, 0, 1e10, 1e10),
            where=lambda props: props.get("class") == 123,
        )
        assert isinstance(dictionary, dict)
        assert len(dictionary) == 1

    @staticmethod
    def test_pquery_all(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for all properties."""
        keys, store = fill_store(store_cls, ":memory:")
        dictionary = store.pquery("*", unique=False)
        assert isinstance(dictionary, dict)
        assert len(dictionary) == len(store)
        assert isinstance(dictionary[keys[0]], dict)

    @staticmethod
    def test_pquery_all_unique_exception(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for all properties."""
        _, store = fill_store(store_cls, ":memory:")
        with pytest.raises(ValueError, match="unique"):
            _ = store.pquery("*", unique=True)

    @staticmethod
    def test_pquery_unique(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(select="props.get('class')")
        assert isinstance(result_set, set)
        assert result_set == {0, 1, 2, 3, 4, None}

    @staticmethod
    def test_pquery_unique_with_geometry(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a geometry intersection."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(
            select="props.get('class')",
            geometry=Polygon.from_bounds(0, 0, 128, 128),
        )
        assert isinstance(result_set, set)
        assert result_set == {0, 1, 2, 3, 4, None}

    @staticmethod
    def test_pquery_unique_with_where(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a where predicate."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(
            select="props.get('class')",
            where="props.get('class') == 1",
        )
        assert isinstance(result_set, set)
        assert result_set == {1}

    @staticmethod
    def test_pquery_unique_with_geometry_and_where(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a geometry and where predicate."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(
            select="props.get('class')",
            geometry=Polygon.from_bounds(0, 0, 128, 128),
            where="props.get('class') == 1",
        )
        assert isinstance(result_set, set)
        assert result_set == {1}

    @staticmethod
    def test_pquery_callable_unique(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a Callable select and where."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(
            select=lambda props: (props.get("class"),),
            where=lambda props: props.get("class") == 1,
            unique=True,
        )
        assert isinstance(result_set, set)
        assert result_set == {1}

    @staticmethod
    def test_pquery_callable_unique_no_squeeze(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a Callable select and where."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(
            select=sample_select,
            where=sample_where_1,
            unique=True,
            squeeze=False,
        )
        assert isinstance(result_set, list)
        assert result_set == [{1}]

    @staticmethod
    def test_pquery_callable_unique_multi_select(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying unique properties with a Callable select and where."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(
            select=sample_multi_select,
            where=sample_where_1,
            unique=True,
        )
        assert isinstance(result_set, list)
        assert result_set == [{1}, {1}]

    @staticmethod
    def test_pquery_callable(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a Callable select and where."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(
            select=lambda props: props.get("class"),
            where=lambda props: props.get("class") == 1,
            unique=False,
        )
        assert isinstance(result_set, dict)
        assert set(result_set.values()) == {1}

    @staticmethod
    def test_pquery_callable_no_where(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with Callable select, no where."""
        _, store = fill_store(store_cls, ":memory:")
        result_set = store.pquery(
            select=lambda props: props.get("class"),
            where=None,
            unique=False,
        )
        assert isinstance(result_set, dict)
        assert set(result_set.values()).issubset({0, 1, 2, 3, 4, None})

    @staticmethod
    def test_pquery_pickled(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a pickled select and where."""
        _, store = fill_store(store_cls, ":memory:")

        result_set = store.pquery(
            select=pickle.dumps(sample_select),
            where=pickle.dumps(sample_where_1),
        )
        assert isinstance(result_set, set)
        assert result_set == {1}

    @staticmethod
    def test_pquery_pickled_no_squeeze(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a pickled select and where."""
        _, store = fill_store(store_cls, ":memory:")

        result_set = store.pquery(
            select=pickle.dumps(sample_select),
            where=pickle.dumps(sample_where_1),
            squeeze=False,
        )
        assert isinstance(result_set, list)
        assert result_set == [{1}]

    @staticmethod
    def test_pquery_pickled_multi_select(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a pickled select and where."""
        _, store = fill_store(store_cls, ":memory:")

        result_set = store.pquery(
            select=pickle.dumps(sample_multi_select),
            where=pickle.dumps(sample_where_1),
        )
        assert isinstance(result_set, list)
        assert result_set == [{1}, {1}]

    @staticmethod
    def test_pquery_invalid_expression_type(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with an invalid expression type."""
        _, store = fill_store(store_cls, ":memory:")
        with pytest.raises(TypeError):
            _ = store.pquery(select=123, where=456)

    @staticmethod
    def test_pquery_non_matching_type(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying with a non-matching type for select and where."""
        _, store = fill_store(store_cls, ":memory:")
        with pytest.raises(TypeError):
            _ = store.pquery(select=123, where="foo")

    @staticmethod
    def test_pquery_dict(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties."""
        _, store = fill_store(store_cls, ":memory:")
        dictionary = store.pquery(select="props.get('class')", unique=False)
        assert isinstance(dictionary, dict)
        assert len(dictionary) == len(store)
        assert all(key in store for key in dictionary)

    @staticmethod
    def test_pquery_dict_with_geometry(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying for properties with a geometry intersection."""
        _, store = fill_store(store_cls, ":memory:")
        dictionary = store.pquery(
            select="props.get('class')",
            unique=False,
            geometry=Polygon.from_bounds(0, 0, 128, 128),
        )
        assert isinstance(dictionary, dict)
        assert len(dictionary) < len(store)
        assert all(key in store for key in dictionary)

    @staticmethod
    def test_is_rectangle(store_cls: type[AnnotationStore]) -> None:
        """Test that _is_rectangle returns True only for rectangles."""
        store = store_cls()

        # Clockwise
        assert store._is_rectangle(
            *[
                (1, 0),
                (0, 0),
                (0, 1),
                (1, 1),
            ],
        )

        # Counter-clockwise
        assert store._is_rectangle(
            *[
                (1, 1),
                (0, 1),
                (0, 0),
                (1, 0),
            ],
        )

        # From shapely
        box = Polygon.from_bounds(0, 0, 10, 10)
        assert store._is_rectangle(*box.exterior.coords)

        # Fuzz
        for _ in range(100):
            box = Polygon.from_bounds(*RNG.integers(0, 100, 4))
            assert store._is_rectangle(*box.exterior.coords)

        # Failure case
        assert not store._is_rectangle(
            *[
                (1, 1.5),
                (0, 1),
                (0, 0),
                (1, 0),
            ],
        )

    @staticmethod
    def test_is_rectangle_invalid_input(
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that _is_rectangle returns False for invalid input."""
        store = store_cls()
        assert not store._is_rectangle(1, 2, 3, 4)
        assert not store._is_rectangle((0, 0), (0, 1), (1, 1), (1, 0), (2, 0))

    @staticmethod
    def test_is_right_angle(
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test that _is_right_angle returns True only for right angles."""
        store = store_cls()

        # skipcq
        r"""
        c
        |
        |
        b-----a
        """
        assert store._is_right_angle(
            *[
                (1, 0),
                (0, 0),
                (0, 1),
            ],
        )

        # skipcq
        r"""
        a
        |
        |
        b-----c
        """
        assert store._is_right_angle(
            *[
                (0, 1),
                (0, 0),
                (1, 0),
            ],
        )

        # skipcq
        r"""
           c
            \
             \
        a-----b
        """
        assert not store._is_right_angle(
            *[
                (0, 0),
                (1, 0),
                (0, 1),
            ],
        )

        assert not store._is_right_angle(
            *[
                (1, 0.2),
                (0, 0),
                (0.2, 1),
            ],
        )

    @staticmethod
    def test_box_query_polygon_intersection(store_cls: type[AnnotationStore]) -> None:
        """Test that a box query correctly checks intersections with polygons."""
        store = store_cls()

        # Add a triangle annotation
        store["foo"] = Annotation(Polygon([(0, 10), (10, 10), (10, 0)]))
        # ASCII diagram of the annotation with points labeled from a to
        # c:
        # skipcq
        r"""
        a-----b
         \    |
          \   |
           \  |
            \ |
             \|
              c
        """

        # Query where the bounding boxes overlap but the geometries do
        # not. Should return an empty result.
        # ASCII diagram of the query:
        # skipcq
        r"""
        a-----b
         \    |
          \   |
           \  |
        +--+\ |
        |  | \|
        +--+  c
        """
        result = store.query([0, 0, 4.9, 4.9], geometry_predicate="intersects")
        assert len(result) == 0

        # Query where the bounding boxes overlap and the geometries do.
        # Should return the annotation.
        # ASCII diagram of the query:
        # skipcq
        r"""
        +------+
        a-----b|
        |\    ||
        | \   ||
        |  \  ||
        |   \ ||
        |    \||
        +-----c+
        """
        result = store.query([0, 0, 11, 11], geometry_predicate="intersects")
        assert len(result) == 1

    @staticmethod
    def test_bquery_bounds(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying a store with a bounding box iterable."""
        _, store = fill_store(store_cls, ":memory:")
        dictionary = store.bquery((0, 0, 1e10, 1e10))
        assert isinstance(dictionary, dict)
        assert len(dictionary) == len(store)

    @staticmethod
    def test_validate_equal_lengths(store_cls: type[AnnotationStore]) -> None:
        """Test that equal length lists are valid."""
        store_cls._validate_equal_lengths([1, 2, 3], [1, 2, 3])
        store_cls._validate_equal_lengths()
        with pytest.raises(ValueError, match="equal length"):
            store_cls._validate_equal_lengths([1, 2, 3], [1, 2])

    @staticmethod
    def test_connection_to_path_memory(store_cls: type[AnnotationStore]) -> None:
        """Test converting a :memory: connection to a path."""
        path = store_cls._connection_to_path(":memory:")
        assert path == Path(":memory:")

    @staticmethod
    def test_connection_to_path_type_error(store_cls: type[AnnotationStore]) -> None:
        """Test converting an invalid type connection to a path."""
        with pytest.raises(TypeError):
            _ = store_cls._connection_to_path(123)

    @staticmethod
    def test_connection_to_path_io(
        store_cls: type[AnnotationStore],
        tmp_path: Path,
    ) -> None:
        """Test converting a named file connection to a path."""
        path = tmp_path / "foo"
        with Path.open(path, "w") as fh:
            store_cls._connection_to_path(fh)
            assert path == Path(fh.name)

    @staticmethod
    def test_nquery_boxpoint_boxpoint(
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test simple querying within a neighbourhood.

        Test that a neighbourhood query returns the correct results
        for a simple data store with two points.

        .. code-block:: text

             ^
            3|--****-----+
             |*      *  C|
            2|         * |
             |     B    *|
            1|   A       *
             |          *|
            0+---------*-->
             0   1   2   3

        Query for all points within a distance of 2 from A. Should
        return a dictionary with a single key, "A", and a value of
        {"B": B}.

        """
        store: AnnotationStore = store_cls()
        ann_a = Annotation(
            Point(1, 1),
            {"class": "A"},
        )
        store["A"] = ann_a
        ann_b = Annotation(
            Point(1.4, 1.4),
            {"class": "B"},
        )
        store["B"] = ann_b
        # C is inside the bounding box of the radius around A but is not
        # returned because it is not inside of the radius.
        ann_c = Annotation(
            Point(2.9, 2.9),
            {"class": "C"},
        )
        store["C"] = ann_c
        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] != 'A'",
            distance=2,
            mode="boxpoint-boxpoint",
        )
        assert isinstance(result, dict)
        assert len(result) == 1
        assert "A" in result
        assert result["A"] == {"B": ann_b}

    @staticmethod
    def test_nquery_boxpoint_boxpoint_no_results(
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying within a neighbourhood with no results.

        Test that a neighbourhood query returns an empty dictionary
        when there are no results.

        .. code-block:: text

            3^
            2|
            1|
            0+----->
             0 1 2 3

        Query for all points within a distance of 2 from A. Should
        return an empty dictionary.

        """
        store: AnnotationStore = store_cls()
        ann_a = Annotation(
            Point(1, 1),
            {"class": "A"},
        )
        store["A"] = ann_a
        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] == 'B'",
            distance=2,
            mode="boxpoint-boxpoint",
        )
        assert isinstance(result, dict)
        assert len(result) == 0

    @staticmethod
    def test_nquery_boxpoint_boxpoint_multiple(
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying within a neighbourhood with multiple results.

        Test that a neighbourhood query returns the correct results
        for a simple data store with four points.

        .. code-block:: text

            3^
            2|   B
            1| A C D <-- D is outside the neighbourhood
            0+------>
             0 1 2 3

        Query for all points within a distance of 2 from A. Should
        return a dictionary with a single key, "A", and a value of
        {"B": B, "C": C}.

        """
        store: AnnotationStore = store_cls()
        ann_a = Annotation(
            Point(1, 1),
            {"class": "A"},
        )
        store["A"] = ann_a

        ann_b = Annotation(
            Point(2, 2),
            {"class": "B"},
        )
        store["B"] = ann_b

        ann_c = Annotation(
            Point(2, 1),
            {"class": "C"},
        )
        store["C"] = ann_c

        ann_d = Annotation(
            Point(3, 1),
            {"class": "D"},
        )
        store["D"] = ann_d

        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="(props['class'] == 'B') | (props['class'] == 'C')",
            distance=2,
            mode="boxpoint-boxpoint",
        )
        assert isinstance(result, dict)
        assert len(result) == 1
        assert "A" in result
        assert result["A"] == {"B": ann_b, "C": ann_c}

    @staticmethod
    def test_nquery_poly_poly(store_cls: type[AnnotationStore]) -> None:
        """Test querying within a neighbourhood with multiple results.

        Test that a neighbourhood query returns the correct results
        for a simple data store with two polygons.

        .. code-block:: text

            3^
            2|   B
            1| A
            0+------>
             0 1 2 3

        """
        store: AnnotationStore = store_cls()

        ann_a = Annotation(  # Triangle
            Polygon([(0, 0), (0, 1), (1, 0)]),
            {"class": "A"},
        )
        store["A"] = ann_a

        ann_b = Annotation(  # Square
            Polygon.from_bounds(1, 1, 2, 2),
            {"class": "B"},
        )
        store["B"] = ann_b

        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] == 'B'",
            distance=2,
            mode="poly-poly",
        )
        assert isinstance(result, dict)
        assert len(result) == 1

    @staticmethod
    def test_nquery_poly_poly_vs_boxpoint_boxpoint(
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying within a neighbourhood with two polygons.

        Test that a full polygon neighbourhood query returns results
        where a centroid query would return no results.

        .. code-block:: text

             ^
            3|
             |         <----2---->
            2|     +-----+     +-----+
             |     |  +  |<-1->|  +  |
            1|     +-----+     +-----+
             |
            0+------------------------>
             0     1     2     3     4

        """
        store: AnnotationStore = store_cls()

        ann_a = Annotation(
            Polygon.from_bounds(1, 1, 2, 2),
            {"class": "A"},
        )
        store["A"] = ann_a

        ann_b = Annotation(
            Polygon.from_bounds(3, 1, 4, 2),
            {"class": "B"},
        )
        store["B"] = ann_b

        distance = 1.25

        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] == 'B'",
            distance=distance,
            mode="boxpoint-boxpoint",
        )
        assert isinstance(result, dict)
        assert len(result) == 0

        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] == 'B'",
            distance=distance,
            mode=("poly", "poly"),
        )
        assert isinstance(result, dict)
        assert len(result) == 1

    @staticmethod
    def test_nquery_polygon_boundary_alt(store_cls: type[AnnotationStore]) -> None:
        """Test querying within a neighbourhood with two polygons.

        This test is similar to test_nquery_polygon_boundary, but
        the centroids are closer than the boundaries.

        .. code-block:: text

             ^
            5|     +-----------------+
             |     +---------------+ |
            4|        <-----2----->| |  centroid-boundary = 2
             |        <--1-->      | |  centroid-centroid = 1
            3|     +-----+         | |
             |     |  +  |  +  ^   | |  centroid-boundary = 2
            2|     +-----+     |   | |
             |        ^        |2  | |
            1|        v1.5     v   | |  boundary-boundary = 1.5
             |     +---------------+ |
            0+-----+-----------------+-->
             0     1     2     3     4
        """
        store: AnnotationStore = store_cls()

        # Annotation A: A 1x1 box
        ann_a = Annotation(
            Polygon.from_bounds(1, 2, 2, 3),
            {"class": "A"},
        )
        store["A"] = ann_a

        # C shaped polygon around annotation A
        ann_b = Annotation(
            Polygon(
                [
                    (1, 0),
                    (4, 0),
                    (4, 5),
                    (1, 5),
                    (1, 4.5),
                    (3.5, 4.5),
                    (3.5, 0.5),
                    (1, 0.5),
                ],
            ),
            {"class": "B"},
        )
        store["B"] = ann_b

        distance = 1.75

        centroid = Polygon.from_bounds(*ann_b.geometry.bounds).centroid

        print(centroid)
        print(ann_a.geometry.centroid)
        print(
            centroid.buffer(distance)
            .intersection(ann_a.geometry.centroid.buffer(distance))
            .area,
        )

        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] == 'B'",
            distance=distance,
            mode="boxpoint-boxpoint",
        )
        assert isinstance(result, dict)
        assert len(result) == 1

    @staticmethod
    def test_nquery_overlapping_grid_box_box(store_cls: type[AnnotationStore]) -> None:
        r"""Find duplicate (overlapping) cell boundaries via bounding boxes.

        This generates an :math:`n \\times n` (where :math:`n=10`) grid
        of overlapping fake cell boundary polygons, where each polygon
        has radius of 5 and the grid has a spacing of 30.

        The grid is then queried with a "box-box" neighbourhood query
        (intersection of bounding boxes) and a `distance` paramete of 0
        (no expansion of bounding boxes).

        """
        store: AnnotationStore = store_cls()

        grid_size = 10
        spacing = 30
        radius = 5
        grid = np.ndindex((grid_size, grid_size))

        for x, y in grid:
            cell_a = cell_polygon(
                (x * spacing + radius, y * spacing + radius),
                radius=radius,
            )
            ann_a = Annotation(cell_a, {"class": "A"})
            cell_b = cell_polygon(
                (x * spacing + radius, y * spacing + radius),
                radius=radius,
            )
            ann_b = Annotation(cell_b, {"class": "B"})

            store[f"A_{x}_{y}"] = ann_a
            store[f"B_{x}_{y}"] = ann_b

        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] == 'B'",
            distance=0,
            mode="box-box",
        )
        assert isinstance(result, dict)
        assert len(result) == grid_size**2
        for v in result.values():
            assert len(v) == 1

    @staticmethod
    def test_nquery_overlapping_grid_boxpoint_boxpoint(
        store_cls: type[AnnotationStore],
    ) -> None:
        r"""Find duplicate (overlapping) cell boundaries via bbox centroid distance.

        This generates an :math:`n \\times n` (where :math:`n=10`) grid
        of overlapping fake cell boundary polygons, where each polygon
        has radius of 5 and the grid has a spacing of 30.

        The grid is then queried with a "boxpoint-boxpoint"
        neighbourhood query and a `distance` of 2 (use a buffer of 2
        around the point).

        """
        store: AnnotationStore = store_cls()

        grid_size = 10
        spacing = 10
        radius = 5
        grid = np.ndindex((grid_size, grid_size))

        for x, y in grid:
            cell_a = cell_polygon(
                (x * spacing + radius, y * spacing + radius),
                radius=radius,
            )
            ann_a = Annotation(cell_a, {"class": "A"})
            cell_b = cell_polygon(
                (x * spacing + radius, y * spacing + radius),
                radius=radius,
            )
            ann_b = Annotation(cell_b, {"class": "B"})

            store[f"A_{x}_{y}"] = ann_a
            store[f"B_{x}_{y}"] = ann_b

        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] == 'B'",
            distance=2,
            mode="boxpoint-boxpoint",
        )
        assert isinstance(result, dict)
        assert len(result) == grid_size**2
        for v in result.values():
            assert len(v) == 1

    @staticmethod
    def test_nquery_overlapping_grid_poly_poly(
        store_cls: type[AnnotationStore],
    ) -> None:
        r"""Find duplicate (overlapping) cell boundaries via polygon intersection.

        This generates an :math:`n \\times n` (where :math:`n=10`) grid
        of overlapping fake cell boundary polygons, where each polygon
        has radius of 5 and the grid has a spacing of 30.

        The grid is then queried with a "poly-poly" neighbourhood query
        (intersection of polygons) and a `distance` parameter of 2.

        """
        store: AnnotationStore = store_cls()

        grid_size = 10
        spacing = 30
        radius = 5
        grid = np.ndindex((grid_size, grid_size))

        for x, y in grid:
            cell_a = cell_polygon(
                (x * spacing + radius, y * spacing + radius),
                radius=radius,
            )
            ann_a = Annotation(cell_a, {"class": "A"})
            cell_b = cell_polygon(
                (x * spacing + radius, y * spacing + radius),
                radius=radius,
            )
            ann_b = Annotation(cell_b, {"class": "B"})

            store[f"A_{x}_{y}"] = ann_a
            store[f"B_{x}_{y}"] = ann_b

        result = store.nquery(
            where="props['class'] == 'A'",
            n_where="props['class'] == 'B'",
            distance=2,
            mode="poly-poly",
        )
        assert isinstance(result, dict)
        assert len(result) == grid_size**2
        for v in result.values():
            assert len(v) == 1

    @staticmethod
    def test_invalid_mode_type(store_cls: type[AnnotationStore]) -> None:
        """Test invalid mode type for AnnotationStore."""
        store: AnnotationStore = store_cls()

        with pytest.raises(TypeError, match="string or tuple of strings"):
            store.nquery(
                where="props['class'] == 'A'",
                n_where="props['class'] == 'B'",
                distance=2,
                mode=123,
            )

    @staticmethod
    def test_invalid_mode_format(store_cls: type[AnnotationStore]) -> None:
        """Check invalid mode string format raises ValueError."""
        store: AnnotationStore = store_cls()

        with pytest.raises(ValueError, match="must be one of"):
            store.nquery(
                where="props['class'] == 'A'",
                n_where="props['class'] == 'B'",
                distance=2,
                mode="invalid-invalid-invalid",
            )

    @staticmethod
    def test_invalid_mode(store_cls: type[AnnotationStore]) -> None:
        """Check unsupported mode raises ValueError."""
        store: AnnotationStore = store_cls()

        with pytest.raises(ValueError, match="must be one of"):
            store.nquery(
                where="props['class'] == 'A'",
                n_where="props['class'] == 'B'",
                distance=2,
                mode="invalid",
            )

    @staticmethod
    def test_bquery_only_where(store_cls: type[AnnotationStore]) -> None:
        """Test that bquery when only a where predicate is given.

        This simply checks for no exceptions raised about None values.

        """
        store = store_cls()
        assert store.bquery(where="props['foo'] == 'bar'") == {}

    @staticmethod
    def test_query_min_area(
        fill_store: Callable,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test querying with a minimum area."""
        _, store = fill_store(store_cls, ":memory:")
        result = store.query((0, 0, 1000, 1000), min_area=1)
        assert len(result) == 100  # should only get cells, pts are too small

    @staticmethod
    def test_import_transform(
        tmp_path: Path,
        store_cls: type[AnnotationStore],
    ) -> None:
        """Test importing with an application-specific transform."""
        # make a simple example of a .geojson exported from QuPath
        anns = {
            "type": "FeatureCollection",
            "features": [
                {
                    "type": "Feature",
                    "geometry": {
                        "type": "Polygon",
                        "coordinates": [
                            [
                                [1076, 2322.55],
                                [1073.61, 2323.23],
                                [1072.58, 2323.88],
                                [1070.93, 2325.61],
                                [1076, 2322.55],
                            ],
                        ],
                    },
                    "properties": {
                        "object_type": "detection",
                        "isLocked": "false",
                        "measurements": [
                            {
                                "name": "Detection probability",
                                "value": 0.847621500492096,
                            },
                            {"name": "Area µm^2", "value": 27.739423751831055},
                        ],
                    },
                },
            ],
        }
        with (tmp_path / "test_annotations.geojson").open("w") as f:
            json.dump(anns, f)

        def unpack_qupath(ann: Annotation) -> Annotation:
            """Helper function to unpack QuPath measurements."""
            props = ann.properties
            measurements = props.pop("measurements")
            for m in measurements:
                props[m["name"]] = m["value"]
            return ann

        store = store_cls.from_geojson(
            tmp_path / "test_annotations.geojson",
            transform=unpack_qupath,
        )
        assert len(store) == 1
        ann = next(iter(store.values()))
        assert ann.properties == {
            "object_type": "detection",
            "isLocked": "false",
            "Detection probability": 0.847621500492096,
            "Area µm^2": 27.739423751831055,
        }