Mercurial > repos > sanbi-uwc > confil

annotate test/test_runner.py @ 4:eaf51f9aff10 draft

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planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty
author sanbi-uwc
date Mon, 04 Mar 2019 03:28:57 -0500
parents 53a61865e86e
children 2b90d0574ea5
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
parents:
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1 import os
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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3 import pytest
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
parents:
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4 from click.testing import CliRunner
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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6 from confil.confil import confil
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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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
sanbi-uwc
parents:
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9 TEST_DATA_DIR = os.path.join(CURR_DIR, "test_data/")
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
parents:
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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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
sanbi-uwc
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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
sanbi-uwc
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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15 @pytest.fixture(scope="module")
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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16 def cli_runner():
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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17 runner = CliRunner()
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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18 return runner
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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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
sanbi-uwc
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21 def test_runner(cli_runner):
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
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22 result = cli_runner.invoke(confil, ["--paired", FILE_1, FILE_2])
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
parents:
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23 assert result.exit_code == 0