Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/cwltool/tests/util.py @ 0:26e78fe6e8c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:26e78fe6e8c4
1 from __future__ import absolute_import
2
3 import distutils.spawn # pylint: disable=no-name-in-module,import-error
4 import functools
5 import os
6 import sys
7 import shutil
8 import contextlib
9 import tempfile
10 import shutil
11 from typing import Text
12
13 from pkg_resources import (Requirement, ResolutionError, # type: ignore
14 resource_filename)
15 import pytest
16
17 from cwltool.context import LoadingContext, RuntimeContext
18 from cwltool.factory import Factory
19 from cwltool.resolver import Path
20 from cwltool.utils import onWindows, subprocess, windows_default_container_id
21 from cwltool.singularity import is_version_2_6, is_version_3_or_newer
22
23
24 def get_windows_safe_factory(runtime_context=None, # type: RuntimeContext
25 loading_context=None, # type: LoadingContext
26 executor=None # type: Any
27 ): # type: (...) -> Factory
28 if onWindows():
29 if not runtime_context:
30 runtime_context = RuntimeContext()
31 runtime_context.find_default_container = functools.partial(
32 force_default_container, windows_default_container_id)
33 runtime_context.use_container = True
34 runtime_context.default_container = windows_default_container_id
35 return Factory(executor, loading_context, runtime_context)
36
37 def force_default_container(default_container_id, _):
38 return default_container_id
39
40 def get_data(filename):
41 # normalizing path depending on OS or else it will cause problem when joining path
42 filename = os.path.normpath(filename)
43 filepath = None
44 try:
45 filepath = resource_filename(
46 Requirement.parse("cwltool"), filename)
47 except ResolutionError:
48 pass
49 if not filepath or not os.path.isfile(filepath):
50 filepath = os.path.join(os.path.dirname(__file__), os.pardir, filename)
51 return Text(Path(filepath).resolve())
52
53
54 needs_docker = pytest.mark.skipif(not bool(distutils.spawn.find_executable('docker')),
55 reason="Requires the docker executable on the "
56 "system path.")
57
58 needs_singularity = pytest.mark.skipif(
59 not bool(distutils.spawn.find_executable('singularity')),
60 reason="Requires the singularity executable on the system path.")
61
62 needs_singularity_2_6 = pytest.mark.skipif(
63 not (distutils.spawn.find_executable('singularity') and is_version_2_6()),
64 reason="Requires that version 2.6.x of singularity executable version is on the system path.")
65
66 needs_singularity_3_or_newer = pytest.mark.skipif(
67 not (distutils.spawn.find_executable('singularity') and is_version_3_or_newer),
68 reason="Requires that version 2.6.x of singularity executable version is on the system path.")
69
70
71 windows_needs_docker = pytest.mark.skipif(
72 onWindows() and not bool(distutils.spawn.find_executable('docker')),
73 reason="Running this test on MS Windows requires the docker executable "
74 "on the system path.")
75
76 def get_main_output(args, env=None):
77 process = subprocess.Popen(
78 [sys.executable, "-m", "cwltool"] + args,
79 stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=env)
80
81 stdout, stderr = process.communicate()
82 return process.returncode, stdout.decode(), stderr.decode()
83
84 @contextlib.contextmanager
85 def temp_dir(suffix=""):
86 c_dir = tempfile.mkdtemp(suffix, dir=os.curdir)
87 try:
88 yield c_dir
89 finally:
90 shutil.rmtree(c_dir, ignore_errors=True)
91
92 @contextlib.contextmanager
93 def working_directory(path):
94 """Change working directory and returns to previous on exit."""
95 prev_cwd = Path.cwd()
96 # before python 3.6 chdir doesn't support paths from pathlib
97 os.chdir(str(path))
98 try:
99 yield
100 finally:
101 os.chdir(str(prev_cwd))