Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_override.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import json |
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2 from io import StringIO |
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3 from typing import Dict, List |
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4 |
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5 import pytest |
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6 |
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7 from cwltool.main import main |
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8 |
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9 from .util import get_data, needs_docker |
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10 |
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11 override_parameters = [ |
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12 ( |
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13 [get_data("tests/override/echo.cwl"), get_data("tests/override/echo-job.yml")], |
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14 {"out": "zing hello1\n"}, |
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15 ), |
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16 ( |
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17 [ |
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18 "--overrides", |
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19 get_data("tests/override/ov.yml"), |
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20 get_data("tests/override/echo.cwl"), |
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21 get_data("tests/override/echo-job.yml"), |
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22 ], |
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23 {"out": "zing hello2\n"}, |
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24 ), |
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25 ( |
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26 [ |
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27 get_data("tests/override/echo.cwl"), |
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28 get_data("tests/override/echo-job-ov.yml"), |
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29 ], |
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30 {"out": "zing hello3\n"}, |
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31 ), |
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32 ([get_data("tests/override/echo-job-ov2.yml")], {"out": "zing hello4\n"}), |
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33 ( |
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34 [ |
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35 "--overrides", |
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36 get_data("tests/override/ov.yml"), |
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37 get_data("tests/override/echo-wf.cwl"), |
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38 get_data("tests/override/echo-job.yml"), |
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39 ], |
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40 {"out": "zing hello2\n"}, |
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41 ), |
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42 ( |
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43 [ |
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44 "--overrides", |
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45 get_data("tests/override/ov2.yml"), |
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46 get_data("tests/override/echo-wf.cwl"), |
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47 get_data("tests/override/echo-job.yml"), |
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48 ], |
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49 {"out": "zing hello5\n"}, |
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50 ), |
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51 ( |
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52 [ |
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53 "--overrides", |
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54 get_data("tests/override/ov3.yml"), |
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55 get_data("tests/override/echo-wf.cwl"), |
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56 get_data("tests/override/echo-job.yml"), |
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57 ], |
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58 {"out": "zing hello6\n"}, |
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59 ), |
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60 ( |
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61 [ |
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62 get_data("tests/override/env-tool_v1.1.cwl"), |
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63 get_data("tests/override/env-tool_cwl-requirement_override.yaml"), |
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64 ], |
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65 {"value": "hello test env"}, |
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66 ), |
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67 ( |
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68 [ |
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69 "--enable-dev", |
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70 get_data("tests/override/env-tool_cwl-requirement_override_default.yaml"), |
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71 ], |
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72 {"value": "hello test env"}, |
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73 ), |
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74 ] |
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75 |
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76 |
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77 @needs_docker |
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78 @pytest.mark.parametrize("parameters,result", override_parameters) |
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79 def test_overrides(parameters: List[str], result: Dict[str, str]) -> None: |
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80 sio = StringIO() |
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81 |
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82 assert main(parameters, stdout=sio) == 0 |
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83 assert json.loads(sio.getvalue()) == result |
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84 |
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85 |
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86 failing_override_parameters = [ |
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87 ( |
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88 [ |
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89 get_data("tests/override/env-tool.cwl"), |
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90 get_data("tests/override/env-tool_cwl-requirement_override.yaml"), |
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91 ], |
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92 "`cwl:requirements` in the input object is not part of CWL v1.0. You can " |
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93 "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to " |
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94 "v1.1", |
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95 ), |
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96 ( |
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97 [ |
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98 get_data("tests/override/env-tool_v1.1.0-dev1.cwl"), |
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99 get_data("tests/override/env-tool_cwl-requirement_override.yaml"), |
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100 ], |
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101 "Version 'v1.1.0-dev1' is a development or deprecated version.\n" |
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102 " Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to " |
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103 "enable support for development and deprecated versions.", |
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104 ), |
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105 ( |
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106 [ |
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107 get_data( |
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108 "tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml" |
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109 ) |
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110 ], |
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111 "`cwl:requirements` in the input object is not part of CWL v1.0. You can " |
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112 "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to " |
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113 "v1.1 or greater.", |
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114 ), |
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115 ( |
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116 [get_data("tests/override/env-tool_cwl-requirement_override_default.yaml")], |
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117 "Version 'v1.1.0-dev1' is a development or deprecated version.\n" |
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118 " Update your document to a stable version (v1.0, v1.1, v1.2) or use --enable-dev to " |
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119 "enable support for development and deprecated versions.", |
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120 ), |
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121 ] |
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122 |
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123 |
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124 @needs_docker |
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125 @pytest.mark.parametrize("parameters,expected_error", failing_override_parameters) |
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126 def test_overrides_fails(parameters: List[str], expected_error: str) -> None: |
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127 sio = StringIO() |
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128 |
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129 assert main(parameters, stderr=sio) == 1 |
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130 stderr = sio.getvalue() |
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131 assert expected_error in stderr, stderr |