def test_memoize_filename_argument_glob(self):
cache = wc_utils.cache.Cache(directory=os.path.join(self.dir, 'cache'))
@cache.memoize(filename_args=[0], filename_kwargs=['input_2'])
def func(input_1, input_2=''):
print('func ran')
with open(input_2, 'r') as file:
return 2 * float(file.read())
fn_1 = os.path.join(self.dir, 'test_1')
fn_2 = os.path.join(self.dir, 'test_2')
with open(fn_1, 'w') as file:
file.write('1')
with open(fn_2, 'w') as file:
file.write('2')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
self.assertEqual(
func(os.path.join(self.dir, 'test_*'), input_2=fn_2), 4)
time.sleep(0.1)
self.assertEqual(captured.stdout.get_text(), 'func ran')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
self.assertEqual(
func(os.path.join(self.dir, 'test_*'), input_2=fn_2), 4)
self.assertEqual(captured.stdout.get_text(), '')
def test_version(self):
with self.App(argv=['-v']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit) as cm:
app.run()
self.assertEqual(cm.exception.code, 0)
stdout = captured.stdout.get_text()
self.assertIn('Test Simulator: 1.2.3', stdout)
self.assertIn('CLI: 4.5.6', stdout)
self.assertIn(
'Python: {}.{}.{}'.format(sys.version_info.major,
sys.version_info.minor,
sys.version_info.micro), stdout)
self.assertEqual(captured.stderr.get_text(), '')
with self.App(argv=['--version']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit) as cm:
app.run()
self.assertEqual(cm.exception.code, 0)
stdout = captured.stdout.get_text()
self.assertIn('Test Simulator: 1.2.3', stdout)
self.assertIn('CLI: 4.5.6', stdout)
self.assertIn(
'Python: {}.{}.{}'.format(sys.version_info.major,
sys.version_info.minor,
sys.version_info.micro), stdout)
self.assertEqual(captured.stderr.get_text(), '')
def test_memoize_with_explicit_name(self):
cache = wc_utils.cache.Cache(directory=os.path.join(self.dir, 'cache'))
@cache.memoize(name='func_1_2')
def func_1(input):
print('func ran')
return 2 * input
@cache.memoize(name='func_1_2')
def func_2(input):
print('func ran')
return 2 * input
@cache.memoize(name='func_3')
def func_3(input):
print('func ran')
return 2 * input
with capturer.CaptureOutput(merged=False, relay=False) as captured:
self.assertEqual(func_1(1), 2)
self.assertEqual(captured.stdout.get_text(), 'func ran')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
self.assertEqual(func_2(1), 2)
self.assertEqual(captured.stdout.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
self.assertEqual(func_3(1), 2)
self.assertEqual(captured.stdout.get_text(), 'func ran')
with self.assertRaises(TypeError):
cache.memoize(name=func_3)
def test_validate(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(
argv=['validate', '2 * abc_a + 3 * abc_b']) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'validate',
'bmp2_a + bmp2_a | x-link: [l-bond-atom: bmp2_a(1)-362S1 | l-displaced-atom: bmp2_a(1)-362H1 | r-bond-atom: bmp2_a(2)-362S1 | r-displaced-atom: bmp2_a(2)-362H1]'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=['validate', 'HELLO']) as app:
app.run()
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=[
'validate',
'abc_a + abc_b | x-link: [l-bond-atom: abc_c(1)-2O1 | l-displaced-atom: abc_d(1)-2H1 | r-bond-atom: abc_b(1)-3C1 | r-displaced-atom: abc_b(1)-3H1 | r-displaced-atom: abc_b(1)-3O1]'
]) as app:
app.run()
def test_run_process_in_container(self):
mgr = self.mgr
mgr.build_container()
# not verbose
mgr.config['verbose'] = False
with capturer.CaptureOutput(relay=False) as capture_output:
mgr.run_process_in_container(['echo', 'here'])
self.assertEqual(capture_output.get_text(), '')
# verbose
mgr.config['verbose'] = True
with capturer.CaptureOutput(relay=False) as capture_output:
mgr.run_process_in_container(['echo', 'here'])
self.assertEqual(capture_output.get_text(), 'here')
# error
mgr.config['verbose'] = False
with self.assertRaisesRegex(wc_env_manager.WcEnvManagerError,
' exit code: 126'):
mgr.run_process_in_container(['__undefined__'])
# error, specified working directory
mgr.config['verbose'] = False
with self.assertRaisesRegex(wc_env_manager.WcEnvManagerError,
' working directory: /root'):
mgr.run_process_in_container(['__undefined__'], work_dir='/root')
# error, specified environment
mgr.config['verbose'] = False
with self.assertRaisesRegex(wc_env_manager.WcEnvManagerError,
' key: val'):
mgr.run_process_in_container(['__undefined__'], env={'key': 'val'})
def test_validate(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=['validate', 'dna', 'ACGT']) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'validate', 'dna',
'ACG[id: "ala" | structure: {}]T'.format(ala_inchi)
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=['validate', 'dna', 'ACGT[']) as app:
# run app
app.run()
def test_get_mol_wt(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'get-molwt', 'abc_a + abc_b', '{abc_a:86, abc_b:57}'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertAlmostEqual(float(captured.stdout.get_text()),
143,
places=0)
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'get-molwt',
'abc_a + abc_b | x-link: [l-bond-atom: abc_a(1)-2O1 | l-displaced-atom: abc_a(1)-2H1+1 | r-bond-atom: abc_b(1)-3C1 | r-displaced-atom: abc_b(1)-3H1 | r-displaced-atom: abc_b(1)-3O1]',
'{abc_a:86, abc_b:57}'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertAlmostEqual(float(captured.stdout.get_text()),
125,
places=0)
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(
argv=['get-molwt', 'HELLO', '{HELLO:86}']) as app:
app.run()
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=[
'get-molwt',
'abc_a + abc_b | x-link: [l-bond-atom: abc_c(1)-2O1 | l-displaced-atom: abc_d(1)-2H1 | r-bond-atom: abc_b(1)-3C1 | r-displaced-atom: abc_b(1)-3H1 | r-displaced-atom: abc_b(1)-3O1]',
'{abc_a:86, abc_b:57}'
]) as app:
app.run()
with self.assertRaisesRegex(SystemExit,
'^Cannot parse subunit_mol_wts:'):
with __main__.App(
argv=['get-molwt', 'abc_a + abc_b', '{abc_a:86, abc_b}'
]) as app:
app.run()
with self.assertRaisesRegex(
SystemExit, '^Unable to calculate BcForm molecular weights:'):
with __main__.App(
argv=['get-molwt', 'abc_a + abc_b', '{abc_a:86}']) as app:
app.run()
def test_raw_cli(self):
with mock.patch('sys.argv', ['obj-tables', '--help']):
with capturer.CaptureOutput(relay=False):
with self.assertRaises(SystemExit) as context:
__main__.main()
self.assertRegex(context.Exception, 'usage: obj-tables')
with mock.patch('sys.argv', ['obj-tables']):
with capturer.CaptureOutput(relay=False) as capture_output:
__main__.main()
self.assertRegex(capture_output.get_text(), 'usage: obj-tables')
def test_run_process_on_host(self):
mgr = self.mgr
mgr.config['verbose'] = False
with capturer.CaptureOutput(relay=False) as capture_output:
mgr.run_process_on_host(['echo', 'here'])
self.assertEqual(capture_output.get_text(), '')
mgr.config['verbose'] = True
with capturer.CaptureOutput(relay=False) as capture_output:
mgr.run_process_on_host(['echo', 'here'])
self.assertEqual(capture_output.get_text(), 'here')
def test_error(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(Exception):
rna_seq_util.Kallisto()._run('index', ['__undefined__.fasta'], verbose=True)
self.assertNotEqual(captured.stdout.get_text(), '')
self.assertNotEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(Exception):
rna_seq_util.Kallisto()._run('index', ['__undefined__.fasta'], verbose=False)
self.assertEqual(captured.stdout.get_text(), '')
self.assertEqual(captured.stderr.get_text(), '')
def test_get_version(self):
with capturer.CaptureOutput(relay=False, termination_delay=0.1) as capture_output:
with __main__.App(argv=['-v']) as app:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(capture_output.get_text(), obj_tables.__version__)
with capturer.CaptureOutput(relay=False, termination_delay=0.1) as capture_output:
with __main__.App(argv=['--version']) as app:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(capture_output.get_text(), obj_tables.__version__)
def test_get_formula(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'get-formula', 'abc_a + abc_b',
'{abc_a:C5H10O, abc_b:C3H5O}'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'C8H15O2')
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'get-formula',
'abc_a + abc_b | x-link: [l-bond-atom: abc_a(1)-2O1 | l-displaced-atom: abc_a(1)-2H1+1 | r-bond-atom: abc_b(1)-3C1 | r-displaced-atom: abc_b(1)-3H1 | r-displaced-atom: abc_b(1)-3O1]',
'{abc_a:C5H10O, abc_b:C3H5O}'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'C8H13O')
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(
argv=['get-formula', 'HELLO', '{HELLO:C5H10O}']) as app:
app.run()
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=[
'get-formula',
'abc_a + abc_b | x-link: [l-bond-atom: abc_c(1)-2O1 | l-displaced-atom: abc_d(1)-2H1 | r-bond-atom: abc_b(1)-3C1 | r-displaced-atom: abc_b(1)-3H1 | r-displaced-atom: abc_b(1)-3O1]',
'{abc_a:C5H10O, abc_b:C3H5O}'
]) as app:
app.run()
with self.assertRaisesRegex(SystemExit,
'^Cannot parse subunit_formulas:'):
with __main__.App(argv=[
'get-formula', 'abc_a + abc_b', '{abc_a:C5H10O, abc_b}'
]) as app:
app.run()
with self.assertRaisesRegex(SystemExit,
'^Unable to calculate BcForm formula:'):
with __main__.App(
argv=['get-formula', 'abc_a + abc_b', '{abc_a:C5H10O}'
]) as app:
app.run()
def test_version(self):
with __main__.App(argv=['-v']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit):
app.run()
self.assertIn(my_simulator.__version__, captured.stdout.get_text())
self.assertEqual(captured.stderr.get_text(), '')
with __main__.App(argv=['--version']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit):
app.run()
self.assertIn(my_simulator.__version__, captured.stdout.get_text())
self.assertEqual(captured.stderr.get_text(), '')
def test_memoize_tuple(self):
cache = wc_utils.cache.Cache(directory=os.path.join(self.dir, 'cache'))
@cache.memoize()
def func(input):
print('func ran')
return input[0] + input[1]
with capturer.CaptureOutput(merged=False, relay=False) as captured:
self.assertEqual(func((1, 2)), 3)
self.assertEqual(captured.stdout.get_text(), 'func ran')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
self.assertEqual(func((1, 2)), 3)
self.assertEqual(captured.stdout.get_text(), '')
def __init__(self, level=StandardOutputErrorCapturerLevel.c, relay=False, termination_delay=0.01, disabled=False):
"""
Args:
level (:obj:`StandardOutputErrorCapturerLevel`, optional): level at which stdout/stderr should be captured
relay (:obj:`bool`): if :obj:`True`, collect the standard output/error streams and continue to pass
them along. if :obj:`False`, collect the stream, squash them, and do not pass them along.
termination_delay (:obj:`float`, optional): The number of seconds to wait before terminating
the output relay process.
disabled (:obj:`bool`, optional): whether to capture standard output and error
"""
self.level = level
self.relay = relay
self.disabled = disabled
if not self.disabled:
if self.level >= StandardOutputErrorCapturerLevel.c and capturer:
self._captured = capturer.CaptureOutput(merged=True, relay=relay, termination_delay=termination_delay)
else:
self._log = ''
else:
msg = (
'Standard output and error could not be logged because capturer is not installed. '
'To install capturer, install BioSimulators utils with the `logging` option '
'(`pip install biosimulators-utils[logging]`).'
)
warn(msg, StandardOutputNotLoggedWarning)
def test(self):
mgr = self.mgr
config = mgr.config
config['verbose'] = True
mgr.login_docker_hub()
# build base image
#mgr.pull_image(config['base_image']['repo_unsquashed'], config['base_image']['tags'])
#mgr.pull_image(config['base_image']['repo'], config['base_image']['tags'])
mgr.build_base_image()
mgr.push_image(config['base_image']['repo_unsquashed'],
config['base_image']['tags'])
mgr.push_image(config['base_image']['repo'],
config['base_image']['tags'])
# build image
#mgr.pull_image(config['image']['repo'], config['image']['tags'])
mgr.build_image()
mgr.push_image(config['image']['repo'], config['image']['tags'])
# build container
mgr.build_container()
mgr.setup_container()
with capturer.CaptureOutput(relay=True) as capture_output:
mgr.run_process_in_container(['wc-cli', '--help'])
self.assertRegex(capture_output.get_text(),
r'usage: wc-cli \[\-h\]')
def test_setup_container(self):
mgr = self.mgr
mgr.config['verbose'] = True
temp_dir_name = tempfile.mkdtemp()
git.Repo.clone_from('https://github.com/KarrLab/wc_utils.git',
os.path.join(temp_dir_name, 'wc_utils'))
git.Repo.clone_from('https://github.com/KarrLab/wc_kb.git',
os.path.join(temp_dir_name, 'wc_kb'))
mgr.config['container']['paths_to_mount'] = {
temp_dir_name: {
'bind': '/root/host/Documents',
'mode': 'rw',
}
}
mgr.config['container']['python_packages'] = '''
/root/host/Documents/wc_utils
-e /root/host/Documents/wc_kb
'''
mgr.build_container()
with capturer.CaptureOutput(relay=False) as capture_output:
mgr.setup_container()
text = capture_output.get_text()
self.assertRegex(text, r'Processing .*?wc_utils')
self.assertRegex(text, r'Successfully installed .*?wc-utils-')
mgr.run_process_in_container(
['rm', '-r', '/root/host/Documents/wc_kb/wc_kb.egg-info'])
shutil.rmtree(temp_dir_name)
def test_get_notebooks(self):
if os.path.isdir(os.path.expanduser('~/.wc/wc_sandbox/notebooks')):
shutil.rmtree(os.path.expanduser('~/.wc/wc_sandbox/notebooks'))
with __main__.App(argv=['install-packages']) as app:
with mock.patch('subprocess.check_call', return_value=None):
app.run()
with __main__.App(argv=['get-notebooks']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
app.run()
text = captured.stdout.get_text()
self.assertIn('Got notebooks', text)
self.assertIn('- bpforms', text)
self.assertTrue(
os.path.isdir(os.path.expanduser('~/.wc/wc_sandbox/notebooks')))
self.assertTrue(
os.path.isdir(
os.path.expanduser('~/.wc/wc_sandbox/notebooks/bpforms')))
self.assertTrue(
os.path.isfile(
os.path.expanduser(
'~/.wc/wc_sandbox/notebooks/bpforms/1. Introductory tutorial.ipynb'
)))
with __main__.App(argv=['get-notebooks']) as app:
app.run()
def test_build_base_image_verbose(self):
mgr = self.mgr
mgr.config['verbose'] = True
with capturer.CaptureOutput(relay=False) as capture_output:
mgr.build_base_image()
self.assertRegex(capture_output.get_text(),
r'Step 1/\d+ : FROM ubuntu')
def test_tool_help(self):
config = {
'tool': {
'wc_kb': {
'label':
'kb',
'description':
'Framework for knowledge bases for whole-cell models',
},
'wc_lang': {
'label': 'lang',
'description':
'Framework for representing whole-cell models',
},
},
'model': {},
}
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=['tool'], config=config) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertRegex(captured.stdout.get_text(), 'kb')
self.assertRegex(captured.stdout.get_text(), 'lang')
self.assertEqual(captured.stderr.get_text(), '')
def test_build_image(self):
mgr = self.mgr
mgr.config['verbose'] = True
mgr.config['image']['tags'] = ['test']
temp_dir_name = tempfile.mkdtemp()
with open(os.path.join(temp_dir_name, 'a'), 'w') as file:
file.write('ABC')
with open(os.path.join(temp_dir_name, 'b'), 'w') as file:
file.write('DEF')
os.mkdir(os.path.join(temp_dir_name, 'c'))
mgr.config['image']['paths_to_copy'] = {
'a': {
'host': os.path.join(temp_dir_name, 'a'),
'image': '/tmp/a',
},
'b': {
'host': os.path.join(temp_dir_name, 'b'),
'image': '/tmp/b',
},
'c': {
'host': os.path.join(temp_dir_name, 'c'),
'image': '/tmp/c',
},
}
mgr.config['image']['python_packages'] = '''
git+https://github.com/KarrLab/wc_lang.git#egg=wc_lang-0.0.1[all]
git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils-0.0.1[all]
'''
with capturer.CaptureOutput(relay=False) as capture_output:
mgr.build_image()
text = capture_output.get_text()
self.assertRegex(text, 'Successfully installed .*?wc-lang-')
self.assertRegex(text, 'Successfully installed .*?wc-utils-')
self.assertRegex(text, 'Successfully built')
mgr.config['container']['python_packages'] = ''
mgr.config['container']['setup_script'] = ''
mgr.build_container()
mgr.copy_path_from_container('/tmp/a',
os.path.join(temp_dir_name, 'a2'))
mgr.copy_path_from_container('/tmp/b',
os.path.join(temp_dir_name, 'b2'))
mgr.copy_path_from_container('/tmp/c',
os.path.join(temp_dir_name, 'c'))
with open(os.path.join(temp_dir_name, 'a2'), 'r') as file:
self.assertEqual(file.read(), 'ABC')
with open(os.path.join(temp_dir_name, 'b2'), 'r') as file:
self.assertEqual(file.read(), 'DEF')
self.assertTrue(os.path.isdir(os.path.join(temp_dir_name, 'c')))
shutil.rmtree(temp_dir_name)
mgr.stop_container()
mgr.remove_containers()
mgr.remove_image(mgr.config['image']['repo'],
mgr.config['image']['tags'])
def test_stdout(self):
sim = core.Simulation(k_syn=1, k_deg=0.25, verbose=True)
with capturer.CaptureOutput() as captured:
sim.run(value_init=4, time_max=10)
stdout = captured.get_text()
lines = stdout.rstrip().split('\n')
for line in lines:
self.assertRegex(line, r'^Time \d+: \d+ molecules$')
def test_tool_wc_lang(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=['tool', 'lang', '--version']) as app:
# run app
app.run()
self.assertRegex(captured.stdout.get_text(),
r'^\d+\.\d+\.\d+[a-zA-Z0-9]*$')
self.assertEqual(captured.stderr.get_text(), '')
def test_help(self):
with biosimulators_utils.__main__.App(argv=[]) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
app.run()
stdout = captured.stdout.get_text()
self.assertTrue(
stdout.startswith('usage: biosimulators-utils'))
self.assertEqual(captured.stderr.get_text(), '')
def test_validate(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(
argv=['validate', 'canonical_dna', 'ACGT']) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'validate', 'canonical_dna',
('ACG'
'[id: "dI" | structure: "{}"'
' | l-bond-atom: P30'
' | l-displaced-atom: O33-1'
' | r-bond-atom: O34'
' | r-displaced-atom: H34'
' ]'
'T').format(dIMP_smiles)
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(
argv=['validate', 'canonical_dna', 'ACGT[']) as app:
# run app
app.run()
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=[
'validate', 'canonical_dna',
('ACGT'
'[id: "dI" | structure: "{}" | l-displaced-atom: O33-1 ]'
).format(dIMP_smiles)
]) as app:
# run app
app.run()
def test_es_check_svr(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=['es-check-server']) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertNotEqual(captured.stdout.get_text(), '')
self.assertEqual(captured.stderr.get_text(), '')
def test_version(self):
with biosimulators_utils.__main__.App(argv=['-v']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit) as cm:
app.run()
self.assertEqual(cm.exception.code, 0)
stdout = captured.stdout.get_text()
self.assertEqual(stdout, biosimulators_utils.__version__)
self.assertEqual(captured.stderr.get_text(), '')
with biosimulators_utils.__main__.App(argv=['--version']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit) as cm:
app.run()
self.assertEqual(cm.exception.code, 0)
stdout = captured.stdout.get_text()
self.assertEqual(stdout, biosimulators_utils.__version__)
self.assertEqual(captured.stderr.get_text(), '')
def _run_job(db_path, builder_fn, job_id):
# Workaround of the clash between jupyter & capturer
sys.stdout = sys.__stdout__
sys.stderr = sys.__stderr__
start_time = time.time()
cpt = None
global _per_process_db
try:
if _per_process_db is None:
_per_process_db = Database(db_path)
job_setup, config, keys_to_job_ids = _per_process_db.set_running(
job_id)
cpt = capturer.CaptureOutput(relay=job_setup.relay)
cpt.start_capture()
if job_setup.timeout is not None:
thread = threading.Thread(
target=_run_job_timed,
args=(
_per_process_db,
job_id,
builder_fn,
config,
keys_to_job_ids,
start_time,
cpt,
),
)
thread.daemon = True
thread.start()
thread.join(job_setup.timeout)
if thread.is_alive():
t = JobTimeout(job_id, job_setup.timeout)
_per_process_db.set_error(job_id, t.message(),
time.time() - start_time)
return t
else:
_run_job_timed(
_per_process_db,
job_id,
builder_fn,
config,
keys_to_job_ids,
start_time,
cpt,
)
return job_id
except Exception as exception:
t = JobError(job_id, str(exception), traceback.format_exc())
if _per_process_db:
_per_process_db.set_error(
job_id,
t.message(),
time.time() - start_time,
cpt.get_bytes() if cpt else None,
)
return t
def test_command_1(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=['command-1']) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), '...')
self.assertEqual(captured.stderr.get_text(), '...')
def test_exec_archive(self):
with self.App(
argv=['-i', 'path to COMBINE/OMEX archive', '-o', '']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
app.run()
self.assertEqual(captured.stdout.get_text(),
'path to COMBINE/OMEX archive')
self.assertEqual(captured.stderr.get_text(), '')
with self.App(
argv=['-i', '', '-o', 'path to directory to save outputs'
]) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit) as cm:
app.run()
self.assertEqual(cm.exception.code,
'path to directory to save outputs')
self.assertEqual(captured.stdout.get_text(), '')
self.assertEqual(captured.stderr.get_text(), '')
