Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_singularity.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 import distutils.spawn |
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2 import os |
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3 import sys |
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4 from pathlib import Path |
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5 |
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6 from cwltool.main import main |
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7 |
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8 from .util import ( |
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9 get_data, |
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10 get_main_output, |
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11 needs_singularity, |
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12 needs_singularity_2_6, |
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13 working_directory, |
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14 ) |
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15 |
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16 sys.argv = [""] |
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17 |
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18 |
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19 @needs_singularity_2_6 |
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20 def test_singularity_pullfolder(tmp_path: Path) -> None: |
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21 workdir = tmp_path / "working_dir_new" |
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22 workdir.mkdir() |
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23 os.chdir(workdir) |
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24 pullfolder = tmp_path / "pullfolder" |
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25 pullfolder.mkdir() |
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26 env = os.environ.copy() |
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27 env["SINGULARITY_PULLFOLDER"] = str(pullfolder) |
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28 result_code, stdout, stderr = get_main_output( |
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29 [ |
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30 "--singularity", |
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31 get_data("tests/sing_pullfolder_test.cwl"), |
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32 "--message", |
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33 "hello", |
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34 ], |
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35 env=env, |
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36 ) |
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37 print(stdout) |
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38 print(stderr) |
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39 assert result_code == 0 |
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40 image = pullfolder / "debian.img" |
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41 assert image.exists() |
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42 |
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43 |
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44 @needs_singularity |
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45 def test_singularity_workflow(tmp_path: Path) -> None: |
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46 with working_directory(tmp_path): |
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47 error_code, _, stderr = get_main_output( |
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48 [ |
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49 "--singularity", |
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50 "--default-container", |
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51 "debian", |
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52 "--debug", |
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53 get_data("tests/wf/hello-workflow.cwl"), |
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54 "--usermessage", |
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55 "hello", |
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56 ] |
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57 ) |
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58 assert "completed success" in stderr, stderr |
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59 assert error_code == 0 |
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60 |
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61 |
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62 def test_singularity_iwdr() -> None: |
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63 result_code = main( |
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64 [ |
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65 "--singularity", |
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66 "--default-container", |
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67 "debian", |
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68 get_data("tests/wf/iwdr-entry.cwl"), |
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69 "--message", |
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70 "hello", |
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71 ] |
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72 ) |
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73 singularity_installed = bool(distutils.spawn.find_executable("singularity")) |
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74 if singularity_installed: |
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75 assert result_code == 0 |
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76 else: |
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77 assert result_code != 0 |
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78 |
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79 |
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80 @needs_singularity |
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81 def test_singularity_incorrect_image_pull() -> None: |
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82 result_code, _, stderr = get_main_output( |
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83 [ |
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84 "--singularity", |
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85 "--default-container", |
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86 "non-existant-weird-image", |
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87 get_data("tests/wf/hello-workflow.cwl"), |
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88 "--usermessage", |
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89 "hello", |
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90 ] |
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91 ) |
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92 assert result_code != 0 |
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93 |
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94 |
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95 @needs_singularity |
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96 def test_singularity_local(tmp_path: Path) -> None: |
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97 workdir = tmp_path / "working_dir" |
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98 workdir.mkdir() |
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99 os.chdir(workdir) |
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100 result_code, stdout, stderr = get_main_output( |
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101 [ |
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102 "--singularity", |
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103 get_data("tests/sing_pullfolder_test.cwl"), |
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104 "--message", |
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105 "hello", |
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106 ] |
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107 ) |
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108 assert result_code == 0 |
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109 |
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110 |
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111 @needs_singularity_2_6 |
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112 def test_singularity_docker_image_id_in_tool(tmp_path: Path) -> None: |
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113 workdir = tmp_path / "working_dir" |
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114 workdir.mkdir() |
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115 os.chdir(workdir) |
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116 result_code, stdout, stderr = get_main_output( |
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117 [ |
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118 "--singularity", |
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119 get_data("tests/sing_pullfolder_test.cwl"), |
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120 "--message", |
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121 "hello", |
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122 ] |
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123 ) |
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124 result_code1, stdout, stderr = get_main_output( |
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125 ["--singularity", get_data("tests/debian_image_id.cwl"), "--message", "hello"] |
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126 ) |
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127 assert result_code1 == 0 |