Mercurial > repos > shellac > guppy_basecaller
annotate env/lib/python3.7/site-packages/cwltool/tests/test_udocker.py @ 0:26e78fe6e8c4 draft
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author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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1 import pytest |
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2 import sys |
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3 import os |
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4 import subprocess |
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5 from .util import get_data, get_main_output |
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6 import tempfile |
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7 import shutil |
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8 from psutil.tests import TRAVIS |
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9 |
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10 LINUX = sys.platform in ('linux', 'linux2') |
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11 |
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12 |
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13 #@pytest.mark.skipif(not LINUX, reason="LINUX only") |
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14 @pytest.mark.skip("Udocker install is broken, see https://github.com/indigo-dc/udocker/issues/221") |
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15 class TestUdocker: |
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16 udocker_path = None |
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17 |
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18 @classmethod |
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19 def setup_class(cls): |
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20 test_cwd = os.getcwd() |
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21 test_environ = os.environ.copy() |
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22 cls.docker_install_dir = tempfile.mkdtemp() |
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23 os.chdir(cls.docker_install_dir) |
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24 |
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25 url="https://download.ncg.ingrid.pt/webdav/udocker/udocker-1.1.3.tar.gz" |
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26 install_cmds = [ |
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27 ["curl", url, "-o", "./udocker-tarball.tgz"], |
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28 ["tar", "xzvf", "udocker-tarball.tgz", "udocker"], |
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29 ["bash", "-c", "UDOCKER_TARBALL={}/udocker-tarball.tgz ./udocker install".format(cls.docker_install_dir)]] |
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30 |
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31 os.environ['UDOCKER_DIR'] = os.path.join(cls.docker_install_dir, ".udocker") |
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32 os.environ['HOME'] = cls.docker_install_dir |
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33 |
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34 results = [] |
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35 for _ in range(3): |
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36 results = [subprocess.call(cmds) for cmds in install_cmds] |
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37 if sum(results) == 0: |
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38 break |
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39 subprocess.call(["rm", "./udocker"]) |
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40 |
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41 assert sum(results) == 0 |
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42 |
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43 cls.udocker_path = os.path.join(cls.docker_install_dir, 'udocker') |
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44 os.chdir(test_cwd) |
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45 os.environ = test_environ |
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46 print('Udocker install dir: ' + cls.docker_install_dir) |
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47 |
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48 @classmethod |
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49 def teardown_class(cls): |
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50 shutil.rmtree(cls.docker_install_dir) |
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51 |
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52 def test_udocker_usage_should_not_write_cid_file(self, tmpdir): |
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53 cwd = tmpdir.chdir() |
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54 |
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55 test_file = "tests/wf/wc-tool.cwl" |
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56 job_file = "tests/wf/wc-job.json" |
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57 error_code, stdout, stderr = get_main_output( |
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58 ["--debug", "--default-container", "debian", "--user-space-docker-cmd=" + self.udocker_path, |
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59 get_data(test_file), get_data(job_file)]) |
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60 cwd.chdir() |
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61 cidfiles_count = sum(1 for _ in tmpdir.visit(fil="*.cid")) |
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62 |
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63 tmpdir.remove(ignore_errors=True) |
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64 |
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65 assert "completed success" in stderr, stderr |
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66 assert cidfiles_count == 0 |
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67 |
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68 @pytest.mark.skipif(TRAVIS, reason='Not reliable on single threaded test on travis.') |
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69 def test_udocker_should_display_memory_usage(self, tmpdir): |
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70 cwd = tmpdir.chdir() |
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71 error_code, stdout, stderr = get_main_output( |
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72 ["--enable-ext", "--default-container=debian", "--user-space-docker-cmd=" + self.udocker_path, |
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73 get_data("tests/wf/timelimit.cwl"), "--sleep_time", "10"]) |
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74 cwd.chdir() |
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75 tmpdir.remove(ignore_errors=True) |
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76 |
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77 assert "completed success" in stderr, stderr |
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78 assert "Max memory" in stderr, stderr |