Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_secrets.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 shutil |
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2 import tempfile |
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3 from io import StringIO |
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4 from typing import Callable, Dict, List, Tuple, Union |
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5 |
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6 import pytest |
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7 |
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8 from cwltool.main import main |
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9 from cwltool.secrets import SecretStore |
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10 from cwltool.utils import CWLObjectType |
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11 |
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12 from .util import get_data, needs_docker, needs_singularity |
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13 |
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14 |
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15 @pytest.fixture |
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16 def secrets() -> Tuple[SecretStore, CWLObjectType]: |
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17 """Fixture to return a secret store.""" |
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18 sec_store = SecretStore() |
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19 job: CWLObjectType = {"foo": "bar", "baz": "quux"} |
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20 |
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21 sec_store.store(["foo"], job) |
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22 return sec_store, job |
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23 |
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24 |
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25 def test_obscuring(secrets: Tuple[SecretStore, CWLObjectType]) -> None: |
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26 """Basic test of secret store.""" |
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27 storage, obscured = secrets |
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28 assert obscured["foo"] != "bar" |
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29 assert obscured["baz"] == "quux" |
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30 result = storage.retrieve(obscured) |
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31 assert isinstance(result, dict) and result["foo"] == "bar" |
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32 |
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33 |
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34 obscured_factories_expected = [ |
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35 ((lambda x: "hello %s" % x), "hello bar"), |
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36 ((lambda x: ["echo", "hello %s" % x]), ["echo", "hello bar"]), |
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37 ((lambda x: {"foo": x}), {"foo": "bar"}), |
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38 ] |
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39 |
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40 |
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41 @pytest.mark.parametrize("factory,expected", obscured_factories_expected) |
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42 def test_secrets( |
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43 factory: Callable[[str], CWLObjectType], |
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44 expected: Union[str, List[str], Dict[str, str]], |
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45 secrets: Tuple[SecretStore, CWLObjectType], |
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46 ) -> None: |
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47 storage, obscured = secrets |
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48 obs = obscured["foo"] |
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49 assert isinstance(obs, str) |
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50 pattern = factory(obs) |
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51 assert pattern != expected |
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52 |
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53 assert storage.has_secret(pattern) |
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54 assert storage.retrieve(pattern) == expected |
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55 |
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56 assert obscured["foo"] != "bar" |
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57 assert obscured["baz"] == "quux" |
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58 |
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59 |
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60 @needs_docker |
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61 def test_secret_workflow_log() -> None: |
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62 stream = StringIO() |
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63 tmpdir = tempfile.mkdtemp() |
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64 main( |
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65 [ |
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66 "--debug", |
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67 "--enable-ext", |
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68 "--outdir", |
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69 tmpdir, |
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70 get_data("tests/wf/secret_wf.cwl"), |
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71 "--pw", |
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72 "Hoopla!", |
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73 ], |
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74 stderr=stream, |
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75 ) |
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76 |
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77 shutil.rmtree(tmpdir) |
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78 assert "Hoopla!" not in stream.getvalue() |
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79 |
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80 |
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81 @needs_singularity |
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82 def test_secret_workflow_log_singularity() -> None: |
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83 stream = StringIO() |
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84 tmpdir = tempfile.mkdtemp() |
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85 main( |
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86 [ |
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87 "--debug", |
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88 "--outdir", |
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89 tmpdir, |
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90 "--singularity", |
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91 get_data("tests/wf/secret_wf.cwl"), |
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92 "--pw", |
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93 "Hoopla!", |
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94 ], |
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95 stderr=stream, |
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96 ) |
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97 |
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98 shutil.rmtree(tmpdir) |
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99 assert "Hoopla!" not in stream.getvalue() |
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100 |
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101 |
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102 @needs_docker |
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103 def test_secret_workflow_log_override() -> None: |
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104 stream = StringIO() |
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105 tmpdir = tempfile.mkdtemp() |
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106 main( |
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107 [ |
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108 "--debug", |
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109 "--outdir", |
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110 tmpdir, |
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111 "--enable-ext", |
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112 "--overrides", |
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113 get_data("tests/wf/override-no-secrets.yml"), |
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114 get_data("tests/wf/secret_wf.cwl"), |
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115 "--pw", |
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116 "Hoopla!", |
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117 ], |
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118 stderr=stream, |
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119 ) |
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120 shutil.rmtree(tmpdir) |
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121 |
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122 assert "Hoopla!" in stream.getvalue() |