Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_udocker.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Test optional udocker feature.""" |
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2 import copy |
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3 import os |
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4 import subprocess |
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5 import sys |
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6 from pathlib import Path |
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7 |
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8 import pytest |
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9 from _pytest.tmpdir import TempPathFactory |
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10 |
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11 from .util import get_data, get_main_output |
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12 |
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13 LINUX = sys.platform in ("linux", "linux2") |
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14 |
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15 |
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16 @pytest.fixture(scope="session") |
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17 def udocker(tmp_path_factory: TempPathFactory) -> str: |
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18 """Udocker fixture, returns the path to the udocker script.""" |
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19 test_cwd = os.getcwd() |
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20 test_environ = copy.copy(os.environ) |
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21 docker_install_dir = str(tmp_path_factory.mktemp("udocker")) |
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22 os.chdir(docker_install_dir) |
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23 |
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24 url = "https://raw.githubusercontent.com/jorge-lip/udocker-builds/master/tarballs/udocker-1.1.4.tar.gz" |
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25 install_cmds = [ |
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26 ["curl", url, "-o", "./udocker-tarball.tgz"], |
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27 ["tar", "xzvf", "udocker-tarball.tgz", "udocker"], |
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28 [ |
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29 "bash", |
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30 "-c", |
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31 "UDOCKER_TARBALL={}/udocker-tarball.tgz ./udocker install".format( |
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32 docker_install_dir |
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33 ), |
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34 ], |
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35 ] |
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36 |
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37 test_environ["UDOCKER_DIR"] = os.path.join(docker_install_dir, ".udocker") |
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38 test_environ["HOME"] = docker_install_dir |
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39 |
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40 results = [] |
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41 for _ in range(3): |
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42 results = [subprocess.call(cmds, env=test_environ) for cmds in install_cmds] |
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43 if sum(results) == 0: |
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44 break |
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45 subprocess.call(["rm", "./udocker"]) |
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46 |
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47 assert sum(results) == 0 |
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48 |
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49 udocker_path = os.path.join(docker_install_dir, "udocker") |
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50 os.chdir(test_cwd) |
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51 return udocker_path |
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52 |
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53 |
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54 @pytest.mark.skipif(not LINUX, reason="LINUX only") |
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55 def test_udocker_usage_should_not_write_cid_file(udocker: str, tmp_path: Path) -> None: |
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56 """Confirm that no cidfile is made when udocker is used.""" |
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57 cwd = Path.cwd() |
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58 os.chdir(tmp_path) |
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59 |
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60 test_file = "tests/wf/wc-tool.cwl" |
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61 job_file = "tests/wf/wc-job.json" |
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62 error_code, stdout, stderr = get_main_output( |
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63 [ |
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64 "--debug", |
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65 "--default-container", |
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66 "debian", |
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67 "--user-space-docker-cmd=" + udocker, |
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68 get_data(test_file), |
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69 get_data(job_file), |
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70 ] |
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71 ) |
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72 |
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73 cidfiles_count = sum(1 for _ in tmp_path.glob("*.cid")) |
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74 os.chdir(cwd) |
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75 |
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76 assert "completed success" in stderr, stderr |
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77 assert cidfiles_count == 0 |
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78 |
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79 |
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80 @pytest.mark.skipif( |
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81 not LINUX or "GITHUB" in os.environ, |
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82 reason="Linux only", |
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83 ) |
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84 def test_udocker_should_display_memory_usage(udocker: str, tmp_path: Path) -> None: |
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85 """Confirm that memory ussage is logged even with udocker.""" |
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86 cwd = Path.cwd() |
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87 os.chdir(tmp_path) |
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88 error_code, stdout, stderr = get_main_output( |
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89 [ |
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90 "--enable-ext", |
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91 "--default-container=debian", |
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92 "--user-space-docker-cmd=" + udocker, |
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93 get_data("tests/wf/timelimit.cwl"), |
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94 "--sleep_time", |
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95 "10", |
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96 ] |
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97 ) |
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98 os.chdir(cwd) |
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99 |
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100 assert "completed success" in stderr, stderr |
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101 assert "Max memory" in stderr, stderr |