Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/tests/util.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 from __future__ import absolute_import
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2
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3 import distutils.spawn # pylint: disable=no-name-in-module,import-error
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4 import functools
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5 import os
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6 import sys
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7 import shutil
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8 import contextlib
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9 import tempfile
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10 import shutil
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11 from typing import Text
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12
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13 from pkg_resources import (Requirement, ResolutionError, # type: ignore
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14 resource_filename)
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15 import pytest
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16
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17 from cwltool.context import LoadingContext, RuntimeContext
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18 from cwltool.factory import Factory
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19 from cwltool.resolver import Path
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20 from cwltool.utils import onWindows, subprocess, windows_default_container_id
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21 from cwltool.singularity import is_version_2_6, is_version_3_or_newer
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22
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23
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24 def get_windows_safe_factory(runtime_context=None, # type: RuntimeContext
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25 loading_context=None, # type: LoadingContext
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26 executor=None # type: Any
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27 ): # type: (...) -> Factory
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28 if onWindows():
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29 if not runtime_context:
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30 runtime_context = RuntimeContext()
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31 runtime_context.find_default_container = functools.partial(
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32 force_default_container, windows_default_container_id)
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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 def force_default_container(default_container_id, _):
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38 return default_container_id
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39
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40 def get_data(filename):
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41 # normalizing path depending on OS or else it will cause problem when joining path
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42 filename = os.path.normpath(filename)
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43 filepath = None
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44 try:
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45 filepath = resource_filename(
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46 Requirement.parse("cwltool"), filename)
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47 except ResolutionError:
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48 pass
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49 if not filepath or not os.path.isfile(filepath):
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50 filepath = os.path.join(os.path.dirname(__file__), os.pardir, filename)
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51 return Text(Path(filepath).resolve())
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52
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53
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54 needs_docker = pytest.mark.skipif(not bool(distutils.spawn.find_executable('docker')),
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55 reason="Requires the docker executable on the "
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56 "system path.")
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57
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58 needs_singularity = pytest.mark.skipif(
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59 not bool(distutils.spawn.find_executable('singularity')),
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60 reason="Requires the singularity executable on the system path.")
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61
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62 needs_singularity_2_6 = pytest.mark.skipif(
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63 not (distutils.spawn.find_executable('singularity') and is_version_2_6()),
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64 reason="Requires that version 2.6.x of singularity executable version is on the system path.")
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65
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66 needs_singularity_3_or_newer = pytest.mark.skipif(
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67 not (distutils.spawn.find_executable('singularity') and is_version_3_or_newer),
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68 reason="Requires that version 2.6.x of singularity executable version is on the system path.")
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69
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70
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71 windows_needs_docker = pytest.mark.skipif(
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72 onWindows() and not bool(distutils.spawn.find_executable('docker')),
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73 reason="Running this test on MS Windows requires the docker executable "
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74 "on the system path.")
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75
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76 def get_main_output(args, env=None):
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77 process = subprocess.Popen(
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78 [sys.executable, "-m", "cwltool"] + args,
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79 stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env)
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80
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81 stdout, stderr = process.communicate()
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82 return process.returncode, stdout.decode(), stderr.decode()
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83
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84 @contextlib.contextmanager
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85 def temp_dir(suffix=""):
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86 c_dir = tempfile.mkdtemp(suffix, dir=os.curdir)
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87 try:
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88 yield c_dir
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89 finally:
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90 shutil.rmtree(c_dir, ignore_errors=True)
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91
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92 @contextlib.contextmanager
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93 def working_directory(path):
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94 """Change working directory and returns to previous on exit."""
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95 prev_cwd = Path.cwd()
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96 # before python 3.6 chdir doesn't support paths from pathlib
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97 os.chdir(str(path))
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98 try:
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99 yield
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100 finally:
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101 os.chdir(str(prev_cwd))