Mercurial > repos > guerler > springsuite
comparison planemo/lib/python3.7/site-packages/cwltool/tests/test_udocker.py @ 0:d30785e31577 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
| author | guerler |
|---|---|
| date | Fri, 31 Jul 2020 00:18:57 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:d30785e31577 |
|---|---|
| 1 import pytest | |
| 2 import sys | |
| 3 import os | |
| 4 import subprocess | |
| 5 from .util import get_data, get_main_output | |
| 6 import tempfile | |
| 7 import shutil | |
| 8 from psutil.tests import TRAVIS | |
| 9 | |
| 10 LINUX = sys.platform in ('linux', 'linux2') | |
| 11 | |
| 12 | |
| 13 #@pytest.mark.skipif(not LINUX, reason="LINUX only") | |
| 14 @pytest.mark.skip("Udocker install is broken, see https://github.com/indigo-dc/udocker/issues/221") | |
| 15 class TestUdocker: | |
| 16 udocker_path = None | |
| 17 | |
| 18 @classmethod | |
| 19 def setup_class(cls): | |
| 20 test_cwd = os.getcwd() | |
| 21 test_environ = os.environ.copy() | |
| 22 cls.docker_install_dir = tempfile.mkdtemp() | |
| 23 os.chdir(cls.docker_install_dir) | |
| 24 | |
| 25 url="https://download.ncg.ingrid.pt/webdav/udocker/udocker-1.1.3.tar.gz" | |
| 26 install_cmds = [ | |
| 27 ["curl", url, "-o", "./udocker-tarball.tgz"], | |
| 28 ["tar", "xzvf", "udocker-tarball.tgz", "udocker"], | |
| 29 ["bash", "-c", "UDOCKER_TARBALL={}/udocker-tarball.tgz ./udocker install".format(cls.docker_install_dir)]] | |
| 30 | |
| 31 os.environ['UDOCKER_DIR'] = os.path.join(cls.docker_install_dir, ".udocker") | |
| 32 os.environ['HOME'] = cls.docker_install_dir | |
| 33 | |
| 34 results = [] | |
| 35 for _ in range(3): | |
| 36 results = [subprocess.call(cmds) for cmds in install_cmds] | |
| 37 if sum(results) == 0: | |
| 38 break | |
| 39 subprocess.call(["rm", "./udocker"]) | |
| 40 | |
| 41 assert sum(results) == 0 | |
| 42 | |
| 43 cls.udocker_path = os.path.join(cls.docker_install_dir, 'udocker') | |
| 44 os.chdir(test_cwd) | |
| 45 os.environ = test_environ | |
| 46 print('Udocker install dir: ' + cls.docker_install_dir) | |
| 47 | |
| 48 @classmethod | |
| 49 def teardown_class(cls): | |
| 50 shutil.rmtree(cls.docker_install_dir) | |
| 51 | |
| 52 def test_udocker_usage_should_not_write_cid_file(self, tmpdir): | |
| 53 cwd = tmpdir.chdir() | |
| 54 | |
| 55 test_file = "tests/wf/wc-tool.cwl" | |
| 56 job_file = "tests/wf/wc-job.json" | |
| 57 error_code, stdout, stderr = get_main_output( | |
| 58 ["--debug", "--default-container", "debian", "--user-space-docker-cmd=" + self.udocker_path, | |
| 59 get_data(test_file), get_data(job_file)]) | |
| 60 cwd.chdir() | |
| 61 cidfiles_count = sum(1 for _ in tmpdir.visit(fil="*.cid")) | |
| 62 | |
| 63 tmpdir.remove(ignore_errors=True) | |
| 64 | |
| 65 assert "completed success" in stderr, stderr | |
| 66 assert cidfiles_count == 0 | |
| 67 | |
| 68 @pytest.mark.skipif(TRAVIS, reason='Not reliable on single threaded test on travis.') | |
| 69 def test_udocker_should_display_memory_usage(self, tmpdir): | |
| 70 cwd = tmpdir.chdir() | |
| 71 error_code, stdout, stderr = get_main_output( | |
| 72 ["--enable-ext", "--default-container=debian", "--user-space-docker-cmd=" + self.udocker_path, | |
| 73 get_data("tests/wf/timelimit.cwl"), "--sleep_time", "10"]) | |
| 74 cwd.chdir() | |
| 75 tmpdir.remove(ignore_errors=True) | |
| 76 | |
| 77 assert "completed success" in stderr, stderr | |
| 78 assert "Max memory" in stderr, stderr |