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mr-cmr-c
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upgrade udocker
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‎tests/test_udocker.py

Lines changed: 89 additions & 89 deletions
Original file line numberDiff line numberDiff line change
@@ -1,111 +1,111 @@
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"""Test optional udocker feature."""
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import copy
13
import os
24
import shutil
35
import subprocess
46
import sys
5-
import tempfile
67

78
try:
89
from psutil.tests import TRAVIS # type: ignore
910
except ImportError:
1011
TRAVIS = True
1112

1213

13-
import py.path
14+
from pathlib import Path
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from typing import Generator
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1417
import pytest
18+
from _pytest.tmpdir import TempPathFactory
1519

1620
from .util import get_data, get_main_output
1721

1822
LINUX = sys.platform in ("linux", "linux2")
1923

2024

25+
@pytest.fixture(scope="session")
26+
def udocker(tmp_path_factory: TempPathFactory) -> str:
27+
"""Udocker fixture, returns the path to the udocker script."""
28+
test_cwd = os.getcwd()
29+
test_environ = copy.copy(os.environ)
30+
docker_install_dir = str(tmp_path_factory.mktemp("udocker"))
31+
os.chdir(docker_install_dir)
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33+
url = "https://raw.githubusercontent.com/jorge-lip/udocker-builds/master/tarballs/udocker-1.1.4.tar.gz"
34+
install_cmds = [
35+
["curl", url, "-o", "./udocker-tarball.tgz"],
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["tar", "xzvf", "udocker-tarball.tgz", "udocker"],
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[
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"bash",
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"-c",
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"UDOCKER_TARBALL={}/udocker-tarball.tgz ./udocker install".format(
41+
docker_install_dir
42+
),
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],
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]
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46+
os.environ["UDOCKER_DIR"] = os.path.join(docker_install_dir, ".udocker")
47+
os.environ["HOME"] = docker_install_dir
48+
49+
results = []
50+
for _ in range(3):
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results = [subprocess.call(cmds) for cmds in install_cmds]
52+
if sum(results) == 0:
53+
break
54+
subprocess.call(["rm", "./udocker"])
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56+
assert sum(results) == 0
57+
58+
udocker_path = os.path.join(docker_install_dir, "udocker")
59+
os.chdir(test_cwd)
60+
os.environ = test_environ
61+
return udocker_path
62+
63+
2164
@pytest.mark.skipif(not LINUX, reason="LINUX only")
22-
class TestUdocker:
23-
udocker_path = ""
24-
docker_install_dir = ""
25-
26-
@classmethod
27-
def setup_class(cls) -> None:
28-
test_cwd = os.getcwd()
29-
test_environ = os.environ.copy()
30-
cls.docker_install_dir = tempfile.mkdtemp()
31-
os.chdir(cls.docker_install_dir)
32-
33-
url = "https://download.ncg.ingrid.pt/webdav/udocker/udocker-1.1.3.tar.gz"
34-
install_cmds = [
35-
["curl", url, "-o", "./udocker-tarball.tgz"],
36-
["tar", "xzvf", "udocker-tarball.tgz", "udocker"],
37-
[
38-
"bash",
39-
"-c",
40-
"UDOCKER_TARBALL={}/udocker-tarball.tgz ./udocker install".format(
41-
cls.docker_install_dir
42-
),
43-
],
65+
def test_udocker_usage_should_not_write_cid_file(udocker: str, tmp_path: Path) -> None:
66+
"""Confirm that no cidfile is made when udocker is used."""
67+
cwd = Path.cwd()
68+
os.chdir(tmp_path)
69+
70+
test_file = "tests/wf/wc-tool.cwl"
71+
job_file = "tests/wf/wc-job.json"
72+
error_code, stdout, stderr = get_main_output(
73+
[
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"--debug",
75+
"--default-container",
76+
"debian",
77+
"--user-space-docker-cmd=" + udocker,
78+
get_data(test_file),
79+
get_data(job_file),
4480
]
81+
)
4582

46-
os.environ["UDOCKER_DIR"] = os.path.join(cls.docker_install_dir, ".udocker")
47-
os.environ["HOME"] = cls.docker_install_dir
48-
49-
results = []
50-
for _ in range(3):
51-
results = [subprocess.call(cmds) for cmds in install_cmds]
52-
if sum(results) == 0:
53-
break
54-
subprocess.call(["rm", "./udocker"])
55-
56-
assert sum(results) == 0
57-
58-
cls.udocker_path = os.path.join(cls.docker_install_dir, "udocker")
59-
os.chdir(test_cwd)
60-
os.environ = test_environ # type: ignore
61-
print("Udocker install dir: " + cls.docker_install_dir)
62-
63-
@classmethod
64-
def teardown_class(cls) -> None:
65-
shutil.rmtree(cls.docker_install_dir)
66-
67-
def test_udocker_usage_should_not_write_cid_file(
68-
self, tmpdir: py.path.local
69-
) -> None:
70-
cwd = tmpdir.chdir()
71-
72-
test_file = "tests/wf/wc-tool.cwl"
73-
job_file = "tests/wf/wc-job.json"
74-
error_code, stdout, stderr = get_main_output(
75-
[
76-
"--debug",
77-
"--default-container",
78-
"debian",
79-
"--user-space-docker-cmd=" + self.udocker_path,
80-
get_data(test_file),
81-
get_data(job_file),
82-
]
83-
)
84-
cwd.chdir()
85-
cidfiles_count = sum(1 for _ in tmpdir.visit(fil="*.cid"))
86-
87-
tmpdir.remove(ignore_errors=True)
88-
89-
assert "completed success" in stderr, stderr
90-
assert cidfiles_count == 0
91-
92-
@pytest.mark.skipif(
93-
TRAVIS, reason="Not reliable on single threaded test on travis."
83+
cidfiles_count = sum(1 for _ in tmp_path.glob("*.cid"))
84+
os.chdir(cwd)
85+
86+
assert "completed success" in stderr, stderr
87+
assert cidfiles_count == 0
88+
89+
90+
@pytest.mark.skipif(
91+
not LINUX or TRAVIS,
92+
reason="Linux only & not reliable on single threaded test on Travis-CI.",
93+
)
94+
def test_udocker_should_display_memory_usage(udocker: str, tmp_path: Path) -> None:
95+
"""Confirm that memory ussage is logged even with udocker."""
96+
cwd = Path.cwd()
97+
os.chdir(tmp_path)
98+
error_code, stdout, stderr = get_main_output(
99+
[
100+
"--enable-ext",
101+
"--default-container=debian",
102+
"--user-space-docker-cmd=" + udocker,
103+
get_data("tests/wf/timelimit.cwl"),
104+
"--sleep_time",
105+
"10",
106+
]
94107
)
95-
def test_udocker_should_display_memory_usage(self, tmpdir: py.path.local) -> None:
96-
cwd = tmpdir.chdir()
97-
error_code, stdout, stderr = get_main_output(
98-
[
99-
"--enable-ext",
100-
"--default-container=debian",
101-
"--user-space-docker-cmd=" + self.udocker_path,
102-
get_data("tests/wf/timelimit.cwl"),
103-
"--sleep_time",
104-
"10",
105-
]
106-
)
107-
cwd.chdir()
108-
tmpdir.remove(ignore_errors=True)
109-
110-
assert "completed success" in stderr, stderr
111-
assert "Max memory" in stderr, stderr
108+
os.chdir(cwd)
109+
110+
assert "completed success" in stderr, stderr
111+
assert "Max memory" in stderr, stderr

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