import os
import platform
from shutil import copyfile

import numpy as np
import pytest
from numpy import array, array_equal, isnan
from numpy.testing import assert_allclose, assert_equal

from bgen_reader import open_bgen
from bgen_reader import example_filepath
from bgen_reader._environment import BGEN_READER_CACHE_HOME
from bgen_reader.test.write_random import _write_random
from bgen_reader.test.test_bgen_reader import nowrite_permission, noread_permission

def example_filepath2(filename):
    filepath = example_filepath(filename)
    metadata2_path = open_bgen._metadata_path_from_filename(filepath,samples_filepath=None)
    if metadata2_path.exists():
        metadata2_path.unlink()
    return filepath


def test_bgen_samples_inside_bgen():
    data = open_bgen(example_filepath2("haplotypes.bgen"), verbose=False)
    samples = ["sample_0", "sample_1", "sample_2", "sample_3"]
    assert all(data.samples == samples)


def test_typing():
    data = open_bgen(example_filepath2("haplotypes.bgen"), verbose=False)
    with pytest.raises(TypeError):
        data.read(dtype=3)


def test_bgen_samples_not_present():
    data = open_bgen(example_filepath2("complex.23bits.no.samples.bgen"),allow_complex=True, verbose=False)
    samples = ["sample_0", "sample_1", "sample_2", "sample_3"]
    assert all(data.samples == samples)


def test_bgen_samples_specify_samples_file():
    data = open_bgen(
        example_filepath2("complex.23bits.bgen"),
        samples_filepath=example_filepath("complex.sample"),
        allow_complex=True,
        verbose=False,
    )
    samples = ["sample_0", "sample_1", "sample_2", "sample_3"]
    assert all(data.samples == samples)


@pytest.mark.skipif(platform.system() != "Darwin", reason="only reliable on macos")
def test_bgen_samples_outside_bgen_unreadable(tmp_path):
    bgen_filepath = example_filepath2("complex.23bits.bgen")
    samples_filepath = tmp_path / "complex.sample"
    copyfile(example_filepath("complex.sample"), samples_filepath)
    with noread_permission(samples_filepath):
        with pytest.raises(PermissionError):
            open_bgen(bgen_filepath, samples_filepath=samples_filepath, allow_complex=True, verbose=False)


@pytest.mark.skipif(platform.system() != "Darwin", reason="only reliable on macos")
def test_bgen_file_not_readable(tmp_path):
    filepath = tmp_path / "haplotypes.bgen"
    copyfile(example_filepath2("haplotypes.bgen"), filepath)
    with noread_permission(filepath):
        with pytest.raises(PermissionError):
            open_bgen(filepath, verbose=False)


def test_bgen_file_dont_exist():
    with pytest.raises(FileNotFoundError):
        open_bgen("idontexist.bgen", verbose=False)


def test_metafile_not_provided():
    open_bgen(example_filepath2("haplotypes.bgen"), verbose=False)


def test_open_bgen_phased_genotype():
    filepath = example_filepath2("haplotypes.bgen")
    bgen2 = open_bgen(filepath, verbose=False)

    assert_equal(bgen2.chromosomes[0], "1")
    assert_equal(bgen2.ids[0], "SNP1")
    assert_equal(bgen2.nalleles[0], 2)
    assert_equal(bgen2.allele_ids[0], "A,G")
    assert_equal(bgen2.positions[0], 1)
    assert_equal(bgen2.rsids[0], "RS1")

    assert_equal(bgen2.chromosomes[2], "1")
    assert_equal(bgen2.ids[2], "SNP3")
    assert_equal(bgen2.nalleles[2], 2)
    assert_equal(bgen2.allele_ids[2], "A,G")
    assert_equal(bgen2.positions[2], 3)
    assert_equal(bgen2.rsids[2], "RS3")

    assert_equal(bgen2.samples[0], "sample_0")
    assert_equal(bgen2.samples[2], "sample_2")
    assert_equal(bgen2.samples[-1], "sample_3")

    g = bgen2.read((0, 0))
    assert_allclose(g[0, 0, :], [1.0, 0.0, 1.0, 0.0])
    g = bgen2.read((-1, -1))
    assert_allclose(g[0, 0, :], [1.0, 0.0, 0.0, 1.0])


def test_open_bgen_variants_info():
    filepath = example_filepath2("example.32bits.bgen")
    bgen2 = open_bgen(filepath, verbose=False)

    assert_equal(bgen2.chromosomes[0], "01")
    assert_equal(bgen2.ids[0], "SNPID_2")
    assert_equal(bgen2.nalleles[0], 2)
    assert_equal(bgen2.allele_ids[0], "A,G")
    assert_equal(bgen2.positions[0], 2000)
    assert_equal(bgen2.rsids[0], "RSID_2")

    assert_equal(bgen2.chromosomes[7], "01")
    assert_equal(bgen2.ids[7], "SNPID_9")
    assert_equal(bgen2.nalleles[7], 2)
    assert_equal(bgen2.allele_ids[7], "A,G")
    assert_equal(bgen2.positions[7], 9000)
    assert_equal(bgen2.rsids[7], "RSID_9")

    assert_equal(bgen2.chromosomes[-1], "01")
    assert_equal(bgen2.ids[-1], "SNPID_200")
    assert_equal(bgen2.nalleles[-1], 2)
    assert_equal(bgen2.allele_ids[-1], "A,G")
    assert_equal(bgen2.positions[-1], 100001)
    assert_equal(bgen2.rsids[-1], "RSID_200")

    assert_equal(bgen2.samples[0], "sample_001")
    assert_equal(bgen2.samples[7], "sample_008")
    assert_equal(bgen2.samples[-1], "sample_500")

    g = bgen2.read((0, 0))
    assert all(isnan(g[0, 0, :]))

    g = bgen2.read((1, 0))
    a = [0.027802362811705648, 0.00863673794284387, 0.9635608992454505]
    assert_allclose(g[0, 0, :], a)

    b = [
        0.97970582847010945215516,
        0.01947019668749305418287,
        0.00082397484239749366197,
    ]
    g = bgen2.read((2, 1))
    assert_allclose(g[0, 0, :], b)


def test_to_improve_coverage():
    filepath = example_filepath2("example.32bits.bgen")
    bgen2 = open_bgen(filepath, verbose=False)  # Creates metadata2.npz file
    assert_equal(bgen2.ncombinations[-1], 3)
    assert_equal(bgen2.phased[-1], False)
    with open_bgen(filepath) as bgen2:  # Reuses metadata2.npz file
        assert_equal(str(bgen2), "open_bgen('{0}')".format(filepath.name))
        assert_equal(bgen2.nsamples, 500)
        assert_equal(bgen2.nvariants, 199)
        assert_equal(bgen2.shape, (500, 199, 3))
        assert_equal(bgen2.ids[-1], "SNPID_200")
        assert_equal(bgen2.rsids[-1], "RSID_200")
        assert_equal(bgen2.chromosomes[-1], "01")
        assert_equal(bgen2.positions[-1], 100001)
        assert_equal(bgen2.nalleles[-1], 2)
        assert_equal(bgen2.allele_ids[-1], "A,G")
        assert_equal(bgen2.ncombinations[-1], 3)
        assert_equal(bgen2.phased[-1], False)
        assert_equal(bgen2.samples[-1], "sample_500")

        b = [
            0.97970582847010945215516,
            0.01947019668749305418287,
            0.00082397484239749366197,
        ]
        g = bgen2.read((2, 1))
        assert_allclose(g[0, 0, :], b)

        g = bgen2.read()
        assert_allclose(g[2, 1, :], b)

    # confirm that out-of-date metadata2 file will be updated
    metadata2 = open_bgen._metadata_path_from_filename(filepath,samples_filepath=None)
    assert os.path.getmtime(metadata2) >= os.path.getmtime(filepath)
    filepath.touch()
    assert os.path.getmtime(metadata2) <= os.path.getmtime(filepath)
    bgen2 = open_bgen(filepath, verbose=False)  # Creates metadata2.npz file
    assert os.path.getmtime(metadata2) >= os.path.getmtime(filepath)


@pytest.mark.skipif(
    "QCTOOLPATH" not in os.environ, reason="This test requires external QCTOOL"
)
@pytest.mark.slow  # It takes hours to generate data locally.  After that, it takes a few minutes
# to run.
def test_bigfile(verbose=False):
    random_file_tests(nsamples=2500, nvariants=500 * 1000, bits=16)


@pytest.mark.skipif(
    "QCTOOLPATH" not in os.environ, reason="This test requires external QCTOOL"
)
@pytest.mark.slow  # Skipping this one by default because it requires the QCTOOL
def test_small_random_file(verbose=False):
    random_file_tests(
        nsamples=25, nvariants=1000, bits=8, verbose=verbose, overwrite=True
    )


def random_file_tests(nsamples, nvariants, bits, verbose=False, overwrite=False):
    test_data_folder = BGEN_READER_CACHE_HOME / "test_data"
    filepath = test_data_folder / "{0}x{1}.{2}bits.bgen".format(
        nsamples, nvariants, bits
    )
    if overwrite or not filepath.exists():
        _write_random(
            filepath,
            nsamples,
            nvariants,
            bits=bits,
            verbose=verbose,
            cleanup_temp_files=True,
        )
    metadata2_path = open_bgen._metadata_path_from_filename(filepath,samples_filepath=None)
    if metadata2_path.exists():
        metadata2_path.unlink()

    with open_bgen(filepath, verbose=verbose) as bgen2:
        assert bgen2.nsamples == nsamples
        assert bgen2.nvariants == nvariants
        val = bgen2.read(-1)
        assert val.shape == (nsamples, 1, 3)
        mean = np.nanmean(val)
        assert mean != mean or 0 <= mean <= 1


def test_open_bgen_without_metadata():
    filepath = example_filepath2("example.32bits.bgen")
    bgen2 = open_bgen(filepath, verbose=False)
    assert_equal(bgen2.allele_ids[7], "A,G")
    assert_equal(bgen2.samples[-1], "sample_500")


def test_open_bgen_file_notfound():
    with pytest.raises(FileNotFoundError):
        open_bgen("/1/2/3/example.32bits.bgen", verbose=False)


def test_open_bgen_complex():
    filepath = example_filepath2("complex.23bits.bgen")
    bgen2 = open_bgen(filepath,allow_complex=True, verbose=False)

    assert_equal(bgen2.chromosomes[0], "01")
    assert_equal(bgen2.ids[0], "")
    assert_equal(bgen2.nalleles[0], 2)
    assert_equal(bgen2.allele_ids[0], "A,G")
    assert_equal(bgen2.positions[0], 1)
    assert_equal(bgen2.rsids[0], "V1")

    assert_equal(bgen2.chromosomes[7], "01")
    assert_equal(bgen2.ids[7], "")
    assert_equal(bgen2.nalleles[7], 7)
    assert_equal(bgen2.allele_ids[7], "A,G,GT,GTT,GTTT,GTTTT,GTTTTT")
    assert_equal(bgen2.positions[7], 8)
    assert_equal(bgen2.rsids[7], "M8")

    assert_equal(bgen2.chromosomes[-1], "01")
    assert_equal(bgen2.ids[-1], "")
    assert_equal(bgen2.nalleles[-1], 2)
    assert_equal(bgen2.allele_ids[-1], "A,G")
    assert_equal(bgen2.positions[-1], 10)
    assert_equal(bgen2.rsids[-1], "M10")

    assert_equal(bgen2.samples[0], "sample_0")
    assert_equal(bgen2.samples[3], "sample_3")

    g = bgen2.read((0, 0))
    assert_allclose(g[0, 0, :2], [1, 0])
    assert isnan(g[0, 0, 2])

    g = bgen2.read((1, 0))
    assert_allclose(g[0, 0, :3], [1, 0, 0])

    g = bgen2.read((-1, -1))
    assert_allclose(g[0, 0, :5], [0, 0, 0, 1, 0])

    ploidy = bgen2.read(0, return_probabilities=False, return_ploidies=True)
    assert_allclose(ploidy[:, 0], [1, 2, 2, 2])
    ploidy = bgen2.read(-1, return_probabilities=False, return_ploidies=True)
    assert_allclose(ploidy[:, 0], [4, 4, 4, 4])

    assert_equal(bgen2.phased.dtype.name, "bool")
    ideal = array([False, True, True, False, True, True, True, True, False, False])
    assert array_equal(bgen2.phased, ideal)


def test_open_bgen_complex_sample_file():
    bgen2 = open_bgen(
        example_filepath2("complex.23bits.bgen"),
        samples_filepath=example_filepath("complex.sample"),
        allow_complex=True,
        verbose=False,
    )

    assert_equal(bgen2.chromosomes[0], "01")
    assert_equal(bgen2.ids[0], "")
    assert_equal(bgen2.nalleles[0], 2)
    assert_equal(bgen2.allele_ids[0], "A,G")
    assert_equal(bgen2.positions[0], 1)
    assert_equal(bgen2.rsids[0], "V1")

    assert_equal(bgen2.chromosomes[7], "01")
    assert_equal(bgen2.ids[7], "")
    assert_equal(bgen2.nalleles[7], 7)
    assert_equal(bgen2.allele_ids[7], "A,G,GT,GTT,GTTT,GTTTT,GTTTTT")
    assert_equal(bgen2.positions[7], 8)
    assert_equal(bgen2.rsids[7], "M8")

    assert_equal(bgen2.chromosomes[-1], "01")
    assert_equal(bgen2.ids[-1], "")
    assert_equal(bgen2.nalleles[-1], 2)
    assert_equal(bgen2.allele_ids[-1], "A,G")
    assert_equal(bgen2.positions[-1], 10)
    assert_equal(bgen2.rsids[-1], "M10")

    assert_equal(bgen2.samples[0], "sample_0")
    assert_equal(bgen2.samples[3], "sample_3")

    missing, ploidy = bgen2.read(
        2, return_probabilities=False, return_missings=True, return_ploidies=True
    )
    assert_allclose(ploidy[:, 0], [1, 2, 2, 2])
    assert_allclose(missing[:, 0], [0, 0, 0, 0])
    assert_allclose(bgen2.phased, [0, 1, 1, 0, 1, 1, 1, 1, 0, 0])


def test_close_del_with():
    filepath = example_filepath2("example.32bits.bgen")
    with open_bgen(filepath, verbose=False) as bgen2:
        pass
    with pytest.raises(ValueError):
        bgen2.read()

    bgen2 = open_bgen(filepath, verbose=False)
    bgen2.close()
    bgen2.samples
    with pytest.raises(ValueError):
        bgen2.read()


def test_read_max_combinations():
    filepath = example_filepath2("example.32bits.bgen")
    with open_bgen(filepath, verbose=False) as bgen2:
        assert (
            np.mean(np.isnan(bgen2.read())) < 2.1e-05
        )  # main data as only a few missing
        val = bgen2.read(max_combinations=5)
        assert (
            np.mean(np.isnan(val[:, :, :3])) < 2.1e-05
        )  # main data as only a few missing
        assert np.all(np.isnan(val[:, :, 3:]))  # all the extra are NaN
        with pytest.raises(ValueError):
            bgen2.read(max_combinations=2)
        with pytest.raises(ValueError):
            bgen2.read(max_combinations=1)
        with pytest.raises(ValueError):
            bgen2.read(max_combinations=0)


def test_read_dtype_and_order():
    filepath = example_filepath2("example.32bits.bgen")
    bgen2 = open_bgen(filepath, verbose=False)
    full = bgen2.read()
    assert full.dtype == np.float64
    assert full.flags["F_CONTIGUOUS"] and not full.flags["C_CONTIGUOUS"]

    val = bgen2.read(None, dtype="float32", order="C")
    assert val.dtype == np.float32
    assert val.flags["C_CONTIGUOUS"] and not val.flags["F_CONTIGUOUS"]
    assert np.allclose(full, val, equal_nan=True)


def test_read_indexing():
    filepath = example_filepath2("example.32bits.bgen")
    bgen2 = open_bgen(filepath, verbose=False)
    full = bgen2.read()

    val = bgen2.read(22)
    assert np.allclose(full[:, [22]], val, equal_nan=True)

    val = bgen2.read([22])
    assert np.allclose(full[:, [22]], val, equal_nan=True)

    val = bgen2.read([22, 30])
    assert np.allclose(full[:, [22, 30]], val, equal_nan=True)

    val = bgen2.read(slice(10, 30, 2))
    assert np.allclose(full[:, 10:30:2], val, equal_nan=True)

    bool_list = [i % 2 == 0 for i in range(bgen2.nvariants)]
    val = bgen2.read(bool_list)
    assert np.allclose(full[:, bool_list], val, equal_nan=True)

    val = bgen2.read((None, None))
    assert np.allclose(full, val, equal_nan=True)

    val = bgen2.read((22, None))
    assert np.allclose(full[[22], :], val, equal_nan=True)

    val = bgen2.read((22, [11, 9]))
    assert np.allclose(full[[22], :][:, [11, 9]], val, equal_nan=True)

    val = bgen2.read(([22, 30], [11, 9]))
    assert np.allclose(full[[22, 30], :][:, [11, 9]], val, equal_nan=True)

    val = bgen2.read((slice(10, 30, 2), [11, 9]))
    assert np.allclose(full[10:30:2, :][:, [11, 9]], val, equal_nan=True)

    bool_list = [i % 2 == 0 for i in range(bgen2.nsamples)]
    val = bgen2.read((bool_list, [11, 9]))
    assert np.allclose(full[bool_list, :][:, [11, 9]], val, equal_nan=True)

    val = bgen2.read(([-1], [-1]))
    assert np.allclose(full[-1, -1], val, equal_nan=True)

    val = bgen2.read(np.s_[10:30:2, :5])
    assert np.allclose(full[10:30:2, :5, :], val, equal_nan=True)

    # Read no variants
    val, missing, ploidy = bgen2.read([], return_missings=True, return_ploidies=True)
    assert val.shape == (bgen2.nsamples, 0, bgen2.max_combinations)
    assert missing.shape == (bgen2.nsamples, 0)
    assert ploidy.shape == (bgen2.nsamples, 0)

    # Read no samples and no variants
    val, missing, ploidy = bgen2.read(
        ([], []), return_missings=True, return_ploidies=True
    )
    assert val.shape == (0, 0, bgen2.max_combinations)
    assert missing.shape == (0, 0)
    assert ploidy.shape == (0, 0)


def test_read_multiple_returns():
    filepath = example_filepath2("example.32bits.bgen")
    bgen2 = open_bgen(filepath, verbose=False)
    full, full_missing, full_ploidy = bgen2.read(
        return_missings=True, return_ploidies=True
    )

    val, missing = bgen2.read(return_missings=True)
    assert np.allclose(full, val, equal_nan=True)
    assert np.allclose(full_missing, missing, equal_nan=False)

    ploidy = bgen2.read(return_probabilities=False, return_ploidies=True)
    assert np.allclose(full_ploidy, ploidy, equal_nan=False)

    val, missing = bgen2.read((slice(10, 30, 2), [11, 9]), return_missings=True)
    assert np.allclose(full[10:30:2, :][:, [11, 9]], val, equal_nan=True)
    assert np.allclose(full_missing[10:30:2, :][:, [11, 9]], missing, equal_nan=False)

    ploidy = bgen2.read(
        (slice(10, 30, 2), [11, 9]), return_probabilities=False, return_ploidies=True
    )
    assert np.allclose(full_ploidy[10:30:2, :][:, [11, 9]], ploidy, equal_nan=False)


if __name__ == "__main__":
    pytest.main([__file__])
