def test_mini_wf(self):
"""
Test that a mini workflow is executable with cwltool after converting.
Workflow receives string input "foo" and outputs "foo foo\n".
:return:
"""
v1_file = os.path.join(
os.path.dirname(__file__),
'mini_wf_cwl1_{}.cwl'.format(
''.join(random.sample(string.ascii_lowercase, 3))
)
)
d2_file = os.path.join(os.path.dirname(__file__),
'mini_wf_d2.cwl')
CWLConverterFacade(d2_file, output=v1_file)
process = subprocess.Popen(
[sys.executable, "-m", "cwltool", v1_file, "--input", "foo"],
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, _ = process.communicate()
os.remove(v1_file)
self.assertIn("foo foo", str(stdout))
self.assertEqual(process.returncode, 0)
def test_mini_tool(self, mock_stdout):
"""
Test that a mini tool is executable with cwltool after converting.
Workflow receives integer input 1 and outputs "1 1 1\n".
:return:
"""
v1_file = os.path.join(
os.path.dirname(__file__),
'mini_tool_cwl1_{}.json'.format(
''.join(random.sample(string.ascii_lowercase, 3))
)
)
d2_file = os.path.join(os.path.dirname(__file__),
'mini_tool_d2.cwl')
CWLConverterFacade(d2_file,
output=v1_file)
process = subprocess.Popen(
[sys.executable, "-m", "cwltool", v1_file, "--in", "1"],
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, _ = process.communicate()
os.remove(v1_file)
self.assertIn("1 1 1", str(stdout))
self.assertIn("Converting done.", mock_stdout.getvalue())
self.assertEqual(process.returncode, 0)
def test_local_input_platform_output_update(
self, mock_api, mock_load, mock_parse
):
"""
Check if install_app is called if app does not exist
"""
mock_app_wf1 = MagicMock(sevenbridges.App)
mock_app_wf1.raw = {
"id": "a/b/c",
"class": "CommandLineTool",
"cwlVersion": "sbg:draft-2"
}
mock_user = MagicMock(sevenbridges.User)
mock_user.username = "******"
mock_api_instance = mock_api.return_value
mock_api_instance.users.me.return_value = mock_user
mock_api_instance.apps.get.side_effect = mock_app_get_not_found
mock_parse.return_value = mock_app_wf1.raw
mock_load.return_value = mock_app_wf1.raw
CWLConverterFacade("a.cwl", output='a/b/c', validate=False,
decompose=False, update=True)
mock_parse.assert_called()
mock_api_instance.apps.create_revision.assert_not_called()
mock_api_instance.apps.install_app.assert_called_with(
'a/b/c', ANY, api=mock_api_instance
)
mock_api_instance.apps.get.assert_called_with(
'a/b/c',
api=mock_api_instance
)
def test_platform_input_no_output_update_true_prompt(
self, mock_api, mock_parse
):
"""
Check if update true via prompt submits create_revision
"""
mock_app_wf1 = MagicMock(sevenbridges.App)
mock_app_wf1.raw = {
"id": "a/b/c",
"class": "CommandLineTool",
"cwlVersion": "sbg:draft-2"
}
mock_api_instance = mock_api.return_value
mock_api_instance.apps.get.return_value = mock_app_wf1
mock_parse.return_value = mock_app_wf1.raw
CWLConverterFacade("a/b/c", validate=False,
decompose=False, update=False)
mock_parse.assert_called()
mock_api_instance.apps.create_revision.assert_called_once_with(
'a/b/c', ANY, ANY, api=mock_api_instance
)
mock_api_instance.apps.get.assert_called_with('a/b/c',
api=mock_api_instance)
def test_base_command_with_spaces(self, mock_stdout):
"""
baseCommand with spaces should be split into indiviudal components
and run corectly on cwltool.
:return:
"""
v1_file = os.path.join(
os.path.dirname(__file__),
'mini_tool_cwl1_{}.json'.format(
''.join(random.sample(string.ascii_lowercase, 3))
)
)
d2_file = os.path.join(os.path.dirname(__file__),
'tool_base_command_with_spaces_d2.cwl')
CWLConverterFacade(d2_file,
output=v1_file)
process = subprocess.Popen(
[sys.executable, "-m", "cwltool", v1_file],
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, _ = process.communicate()
os.remove(v1_file)
self.assertIn("A test string", str(stdout))
self.assertEqual(process.returncode, 0)
self.assertIn("Converting done.", mock_stdout.getvalue())
def main(args=sys.argv[1:]):
"""
Entrypoint and CLI for sbg_cwl_upgrader tool.
"""
args = vars(create_arg_parser().parse_args(args))
configure_logging(args)
CWLConverterFacade(token=args['token'],
profile=args['profile'],
platform=args['platform'],
endpoint=args['endpoint'],
app_revision=args['revision'],
input_=args['input'],
output=args['output'],
cwl_version=args['cwl_version'],
validate=args['validate'],
update=args['update'],
decompose=args['decompose'])
def test_local_input_no_output(self):
"""
Check exception is raised for local input and no output
"""
with self.assertRaises(Exception):
CWLConverterFacade('wf.cwl')