Mercurial > repos > sanbi-uwc > confil

annotate test/test_runner.py @ 13:bbf9ab2ebee7 draft default tip

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planemo upload for repository https://github.com/COMBAT-TB/confil commit fcda5ac2013e3253d68cb6db06acf3b5450dcd0c
author sanbi-uwc
date Tue, 12 Mar 2019 09:16:35 -0400
parents 5ec97cccb3fe
children
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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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5ec97cccb3fe planemo upload for repository https://github.com/COMBAT-TB/confil commit b1a96c1b50cea70a20d4e606100879da8b6ed1b2
sanbi-uwc
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6 from confil.confil import confil
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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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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/")
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2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
sanbi-uwc
parents: 3
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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
sanbi-uwc
parents:
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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
parents:
diff changeset
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
parents:
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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
parents:
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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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2b90d0574ea5 planemo upload for repository https://github.com/COMBAT-TB/confil commit c84738cfc4876c591d7108229038a4001f836afb
sanbi-uwc
parents: 3
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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
sanbi-uwc
parents:
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22 def test_runner(cli_runner):
53a61865e86e planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
sanbi-uwc
parents:
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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
sanbi-uwc
parents:
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24 assert result.exit_code == 0