Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/tests/util.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000 (2021-03-22)
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1 import contextlib
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2 import distutils.spawn # pylint: disable=no-name-in-module,import-error
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3 import functools
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4 import io
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5 import os
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6 import subprocess
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7 import sys
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8 from pathlib import Path
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9 from typing import Any, Generator, List, Mapping, Optional, Tuple, Union
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10
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11 import pytest
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12 from pkg_resources import Requirement, ResolutionError, resource_filename
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13
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14 from cwltool.context import LoadingContext, RuntimeContext
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15 from cwltool.executors import JobExecutor
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16 from cwltool.factory import Factory
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17 from cwltool.main import main
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18 from cwltool.singularity import is_version_2_6, is_version_3_or_newer
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19 from cwltool.utils import onWindows, windows_default_container_id
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20
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21
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22 def get_windows_safe_factory(
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23 runtime_context: Optional[RuntimeContext] = None,
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24 loading_context: Optional[LoadingContext] = None,
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25 executor: Optional[JobExecutor] = None,
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26 ) -> Factory:
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27 if onWindows():
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28 if not runtime_context:
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29 runtime_context = RuntimeContext()
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30 runtime_context.find_default_container = functools.partial(
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31 force_default_container, windows_default_container_id
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32 )
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33 runtime_context.use_container = True
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34 runtime_context.default_container = windows_default_container_id
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35 return Factory(executor, loading_context, runtime_context)
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36
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37
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38 def force_default_container(default_container_id: str, _: str) -> str:
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39 return default_container_id
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40
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41
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42 def get_data(filename: str) -> str:
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43 # normalizing path depending on OS or else it will cause problem when joining path
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44 filename = os.path.normpath(filename)
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45 filepath = None
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46 try:
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47 filepath = resource_filename(Requirement.parse("cwltool"), filename)
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48 except ResolutionError:
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49 pass
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50 if not filepath or not os.path.isfile(filepath):
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51 filepath = os.path.join(os.path.dirname(__file__), os.pardir, filename)
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52 return str(Path(filepath).resolve())
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53
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54
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55 needs_docker = pytest.mark.skipif(
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56 not bool(distutils.spawn.find_executable("docker")),
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57 reason="Requires the docker executable on the system path.",
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58 )
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59
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60 needs_singularity = pytest.mark.skipif(
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61 not bool(distutils.spawn.find_executable("singularity")),
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62 reason="Requires the singularity executable on the system path.",
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63 )
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64
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65 needs_singularity_2_6 = pytest.mark.skipif(
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66 not bool(distutils.spawn.find_executable("singularity") and is_version_2_6()),
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67 reason="Requires that version 2.6.x of singularity executable version is on the system path.",
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68 )
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69
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70 needs_singularity_3_or_newer = pytest.mark.skipif(
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71 (not bool(distutils.spawn.find_executable("singularity")))
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72 or (not is_version_3_or_newer()),
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73 reason="Requires that version 3.x of singularity executable version is on the system path.",
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74 )
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75
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76
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77 windows_needs_docker = pytest.mark.skipif(
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78 onWindows() and not bool(distutils.spawn.find_executable("docker")),
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79 reason="Running this test on MS Windows requires the docker executable "
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80 "on the system path.",
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81 )
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82
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83
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84 def get_main_output(
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85 args: List[str],
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86 env: Union[
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87 Mapping[bytes, Union[bytes, str]], Mapping[str, Union[bytes, str]], None
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88 ] = None,
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89 monkeypatch: Any = None,
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90 ) -> Tuple[Optional[int], str, str]:
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91 stdout = io.StringIO()
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92 stderr = io.StringIO()
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93 if env is not None:
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94 assert monkeypatch is not None
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95 monkeypatch.setattr(os, "environ", env)
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96 try:
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97 rc = main(argsl=args, stdout=stdout, stderr=stderr)
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98 except SystemExit as e:
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99 rc = e.code
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100 return (
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101 rc,
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102 stdout.getvalue(),
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103 stderr.getvalue(),
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104 )
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105
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106
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107 @contextlib.contextmanager
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108 def working_directory(path: Union[str, Path]) -> Generator[None, None, None]:
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109 """Change working directory and returns to previous on exit."""
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110 prev_cwd = Path.cwd()
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111 os.chdir(path)
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112 try:
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113 yield
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114 finally:
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115 os.chdir(prev_cwd)