"""testing the default import"""

import os

from pathlib import Path
from tempfile import TemporaryDirectory
from unittest import TestCase

import pytest

from cogent3 import app_help, available_apps, get_app, open_data_store
from cogent3.app.composable import LOADER, WRITER, is_app
from cogent3.util.table import Table


def _get_all_composables(tmp_dir_name):
    tmp_dir_name = Path(tmp_dir_name)
    test_model1 = get_app("model", "HKY85")
    test_model2 = get_app("model", "GN")
    test_hyp = get_app("hypothesis", test_model1, test_model2)
    test_num_reps = 100
    return [
        get_app(
            "align_to_ref",
        ),
        get_app("progressive_align", model="GY94"),
        get_app("fast_slow_dist", moltype="dna", fast_calc="hamming"),
        get_app("ancestral_states"),
        get_app("bootstrap", hyp=test_hyp, num_reps=test_num_reps),
        get_app("hypothesis", test_model1, test_model2),
        get_app("model", "GN"),
        get_app("tabulate_stats"),
        get_app("fixed_length", 100),
        get_app("sample.min_length", 100),
        get_app("write_db", open_data_store(tmp_dir_name / "delme.sqlitedb", mode="w")),
        get_app(
            "write_json",
            open_data_store(tmp_dir_name / "json", suffix="json", mode="w"),
        ),
        get_app(
            "write_seqs",
            open_data_store(tmp_dir_name / "fasta", suffix="fasta", mode="w"),
        ),
        get_app("omit_bad_seqs"),
        get_app("omit_degenerates"),
        get_app("omit_duplicated"),
        get_app("take_codon_positions", 1),
        get_app("take_named_seqs"),
        get_app("take_n_seqs", 2),
        get_app("trim_stop_codons", gc=1),
        get_app("select_translatable"),
        get_app("quick_tree"),
        get_app("scale_branches"),
        get_app("uniformize_tree"),
    ]


class TestAvailableApps(TestCase):
    def test_available_apps(self):
        """available_apps returns a table"""
        from cogent3.util.table import Table

        apps = available_apps()
        self.assertIsInstance(apps, Table)
        self.assertTrue(apps.shape[0] > 10)

    def test_composable_pairwise_applications(self):
        """Properly compose two composable applications"""

        with TemporaryDirectory(dir=".") as dirname:
            applications = _get_all_composables(os.path.join(dirname, "delme"))
            for app in applications:
                self.assertTrue(is_app(app), msg=app)

            composable_application_tuples = [
                (app1, app2)
                for app1 in applications
                for app2 in applications
                if app1 != app2
                and (
                    app1._return_types & app2._data_types
                    or app1._return_types & {"SerialisableType", "IdentifierType"}
                )
                and app1.app_type is not WRITER
                and app2.app_type is not LOADER
            ]

            for app_a, app_b in composable_application_tuples:
                app_a.disconnect()
                app_b.disconnect()
                # Compose two composable applications, there should not be exceptions.
                app_a + app_b

    def test_incompatible_pairwise_applications(self):
        """Properly identify two incompatible applications"""

        with TemporaryDirectory(dir=".") as dirname:
            applications = _get_all_composables(os.path.join(dirname, "delme"))
            for app in applications:
                self.assertTrue(is_app(app))

            incompatible_application_tuples = [
                (app1, app2)
                for app1 in applications
                for app2 in applications
                if app1.app_type is WRITER
                or app2.app_type is LOADER
                and app1 != app2
                and not app1._return_types & app2._data_types
                and not app1._return_types & {"SerialisableType", "IdentifierType"}
            ]

            for app_a, app_b in incompatible_application_tuples:
                err_type = ValueError if app_a is app_b else TypeError
                app_a.disconnect()
                app_b.disconnect()

                # Compose two incompatible applications, there should be exceptions.
                with self.assertRaises(err_type):
                    app_a + app_b


@pytest.mark.parametrize("name", ("sample.min_length", "min_length"))
def test_get_app(name):
    app = get_app(name, 500)
    assert app.__class__.__name__.endswith(name.split(".")[-1])


def test_get_app_kwargs():
    # when an app has a name kwarg
    # we should still be able to use get_app!
    _ = get_app("model", "F81", name="F81-model")


def test_app_help(capsys):
    app_help("concat")
    got = capsys.readouterr().out
    assert "Options" in got
    assert got.count("SerialisableType") == 1  # output type


@pytest.mark.parametrize(
    "app_name", ("bootstrap", "from_primitive", "load_db", "take_named_seqs")[:1]
)
def test_app_help_signature(capsys, app_name):
    from cogent3.app import _get_app_matching_name, _make_signature

    with pytest.raises(ValueError, match="app cannot be None"):
        _make_signature(None)

    got = _make_signature(_get_app_matching_name(app_name))
    # app name is in quotes
    assert f'"{app_name}"' in got
    # check split across multiple lines if long signature
    if len(got) > 70:
        assert got.count("\n") > 1


def test_available_apps_filter():
    """available apps can be filtered by name"""
    app_name_filter: str = "load"
    filtered_apps = available_apps(app_name_filter)
    assert isinstance(filtered_apps, Table)
    assert len(filtered_apps) > 0
    # check every returned table row 'name' has filter in it
    assert sum(app_name_filter in n for n in filtered_apps.columns["name"]) == len(
        filtered_apps
    )