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annotate env/lib/python3.7/site-packages/cwltool/tests/test_override.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 import json
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2
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3 from six import StringIO
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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 from cwltool import load_tool
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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 ([get_data('tests/override/echo.cwl'),
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13 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 (["--overrides",
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17 get_data('tests/override/ov.yml'),
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18 get_data('tests/override/echo.cwl'),
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19 get_data('tests/override/echo-job.yml')],
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20 {"out": "zing hello2\n"}
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21 ),
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22 ([get_data('tests/override/echo.cwl'),
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23 get_data('tests/override/echo-job-ov.yml')],
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24 {"out": "zing hello3\n"}
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25 ),
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26 ([get_data('tests/override/echo-job-ov2.yml')],
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27 {"out": "zing hello4\n"}
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28 ),
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29 (["--overrides",
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30 get_data('tests/override/ov.yml'),
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31 get_data('tests/override/echo-wf.cwl'),
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32 get_data('tests/override/echo-job.yml')],
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33 {"out": "zing hello2\n"}
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34 ),
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35 (["--overrides",
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36 get_data('tests/override/ov2.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 {"out": "zing hello5\n"}
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40 ),
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41 (["--overrides",
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42 get_data('tests/override/ov3.yml'),
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43 get_data('tests/override/echo-wf.cwl'),
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44 get_data('tests/override/echo-job.yml')],
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45 {"out": "zing hello6\n"}
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46 ),
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47 ([get_data('tests/override/env-tool_v1.1.cwl'),
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48 get_data('tests/override/env-tool_cwl-requirement_override.yaml')],
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49 {"value": "hello test env"}
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50 ),
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51 (["--enable-dev",
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52 get_data('tests/override/env-tool_cwl-requirement_override_default.yaml')],
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53 {"value": "hello test env"}
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54 ),
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55 ]
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56
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57 @needs_docker
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58 @pytest.mark.parametrize('parameters,result', override_parameters)
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59 def test_overrides(parameters, result):
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60 sio = StringIO()
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61
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62 assert main(parameters, stdout=sio) == 0
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63 assert json.loads(sio.getvalue()) == result
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64
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65
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66 failing_override_parameters = [
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67 ([get_data('tests/override/env-tool.cwl'),
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68 get_data('tests/override/env-tool_cwl-requirement_override.yaml')],
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69 "`cwl:requirements` in the input object is not part of CWL v1.0. You can "
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70 "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to "
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71 "v1.1"
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72 ),
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73 ([get_data('tests/override/env-tool_v1.1.0-dev1.cwl'),
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74 get_data('tests/override/env-tool_cwl-requirement_override.yaml')],
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75 "Version 'v1.1.0-dev1' is a development or deprecated version.\n"
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76 " Update your document to a stable version (v1.0, v1.1) or use --enable-dev to "
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77 "enable support for development and deprecated versions."
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78 ),
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79 ([get_data('tests/override/env-tool_cwl-requirement_override_default_wrongver.yaml')],
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80 "`cwl:requirements` in the input object is not part of CWL v1.0. You can "
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81 "adjust to use `cwltool:overrides` instead; or you can set the cwlVersion to "
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82 "v1.1 or greater."
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83 ),
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84 ([get_data('tests/override/env-tool_cwl-requirement_override_default.yaml')],
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85 "Version 'v1.1.0-dev1' is a development or deprecated version.\n"
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86 " Update your document to a stable version (v1.0, v1.1) or use --enable-dev to "
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87 "enable support for development and deprecated versions."
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88 ),
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89 ]
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90
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91 @needs_docker
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92 @pytest.mark.parametrize('parameters,expected_error', failing_override_parameters)
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93 def test_overrides_fails(parameters, expected_error):
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94 sio = StringIO()
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95
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96 assert main(parameters, stderr=sio) == 1
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97 stderr = sio.getvalue()
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98 assert expected_error in stderr, stderr