view test/test_runner.py @ 10:2cde7c81c694 draft

planemo upload for repository https://github.com/COMBAT-TB/confil commit 036172521321dbafe62e6d72b3a491f4bc4b9dc9-dirty

import os

import pytest
from click.testing import CliRunner

from confil.confil import confil, parse_report

CURR_DIR = os.path.dirname(os.path.abspath(__file__))
TEST_DATA_DIR = os.path.join(CURR_DIR, "test_data/")
TEST_REPORT = os.path.join(TEST_DATA_DIR, "test_file.tab")
FILE_1 = os.path.join(TEST_DATA_DIR, "test_file_1.fastq")
FILE_2 = os.path.join(TEST_DATA_DIR, "test_file_2.fastq")


@pytest.fixture(scope="module")
def cli_runner():
    runner = CliRunner()
    return runner


@pytest.mark.skip(reason="No way of currently testing this. It's KRAKEN!")
def test_runner(cli_runner):
    result = cli_runner.invoke(confil, ["--paired", FILE_1, FILE_2])
    assert result.exit_code == 0


@pytest.mark.parametrize("test_input, expected", [
    (type(parse_report(TEST_REPORT, 50)), list),
    (parse_report(TEST_REPORT, 50)[5], 'Mycobacterium'),
    (parse_report(TEST_REPORT, 50)[0], '55.84')
])
def test_parse_report(test_input, expected):
    assert test_input == expected


def test_parse_report_exception():
    with pytest.raises(SystemExit):
        parse_report(TEST_REPORT, 90)