Mercurial > repos > sanbi-uwc > confil

annotate test/test_runner.py @ 11:72cb19a32d8b draft

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planemo upload for repository https://github.com/COMBAT-TB/confil commit 036172521321dbafe62e6d72b3a491f4bc4b9dc9-dirty
author sanbi-uwc
date Fri, 08 Mar 2019 13:55:10 -0500
parents 2b90d0574ea5
children 5ec97cccb3fe
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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1 import os
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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3 import pytest
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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4 from click.testing import CliRunner
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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6 from confil.confil import confil, parse_report
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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8 CURR_DIR = os.path.dirname(os.path.abspath(__file__))
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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9 TEST_DATA_DIR = os.path.join(CURR_DIR, "test_data/")
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2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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10 TEST_REPORT = os.path.join(TEST_DATA_DIR, "test_file.tab")
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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11 FILE_1 = os.path.join(TEST_DATA_DIR, "test_file_1.fastq")
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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12 FILE_2 = os.path.join(TEST_DATA_DIR, "test_file_2.fastq")
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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15 @pytest.fixture(scope="module")
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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16 def cli_runner():
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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17 runner = CliRunner()
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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18 return runner
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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21 @pytest.mark.skip(reason="No way of currently testing this. It's KRAKEN!")
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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22 def test_runner(cli_runner):
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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23 result = cli_runner.invoke(confil, ["--paired", FILE_1, FILE_2])
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
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24 assert result.exit_code == 0
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2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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27 @pytest.mark.parametrize("test_input, expected", [
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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28 (type(parse_report(TEST_REPORT, 50)), list),
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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29 (parse_report(TEST_REPORT, 50)[5], 'Mycobacterium'),
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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30 (parse_report(TEST_REPORT, 50)[0], '55.84')
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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31 ])
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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32 def test_parse_report(test_input, expected):
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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33 assert test_input == expected
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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36 def test_parse_report_exception():
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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37 with pytest.raises(SystemExit):
2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
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38 parse_report(TEST_REPORT, 90)