def execute(self) -> Tuple[UUID, Dict, Optional[Exception]]:
"""
:return: Run ID, dict with new files, exception if there is any
"""
run_id = uuid4()
runtime_context = RuntimeContext()
runtime_context.outdir = self.file_manager.ROOT_DIRECTORY
runtime_context.basedir = self.file_manager.ROOT_DIRECTORY
runtime_context.default_stdin = subprocess.DEVNULL
runtime_context.default_stdout = subprocess.DEVNULL
runtime_context.default_stderr = subprocess.DEVNULL
os.chdir(self.file_manager.ROOT_DIRECTORY)
factory = Factory(runtime_context=runtime_context)
executable = factory.make(self._workflow_path)
data = {}
for data_file in self._data_paths:
with open(data_file) as f:
new_data = yaml.load(f, Loader=yaml.Loader)
data = {**new_data, **data}
try:
result: Dict = executable(**data)
return run_id, result, None
except Exception as e:
traceback.print_exc(file=sys.stderr)
return run_id, {}, e
def test_sequential_workflow(tmp_path: Path) -> None:
test_file = "tests/wf/count-lines1-wf.cwl"
executor = MultithreadedJobExecutor()
runtime_context = RuntimeContext()
runtime_context.outdir = str(tmp_path)
runtime_context.select_resources = executor.select_resources
factory = get_windows_safe_factory(
executor=executor, runtime_context=runtime_context
)
echo = factory.make(get_data(test_file))
file_contents = {"class": "File", "location": get_data("tests/wf/whale.txt")}
assert echo(file1=file_contents) == {"count_output": 16}
def test_sequential_workflow(tmpdir):
test_file = "tests/wf/count-lines1-wf.cwl"
executor = MultithreadedJobExecutor()
runtime_context = RuntimeContext()
runtime_context.outdir = str(tmpdir)
runtime_context.select_resources = executor.select_resources
factory = get_windows_safe_factory(
executor=executor, runtime_context=runtime_context)
echo = factory.make(get_data(test_file))
file_contents = {"class": "File",
"location": get_data("tests/wf/whale.txt")}
assert echo(file1=file_contents) == {"count_output": 16}
def test_scatter_output_filenames(tmpdir: py.path.local) -> None:
"""If a scatter step produces identically named output then confirm that the final output is renamed correctly."""
cwd = tmpdir.chdir()
rtc = RuntimeContext()
rtc.outdir = str(cwd)
factory = cwltool.factory.Factory(runtime_context=rtc)
output_names = ["output.txt", "output.txt_2", "output.txt_3"]
scatter_workflow = factory.make(get_data("tests/scatter_numbers.cwl"))
result = scatter_workflow(range=3)
assert isinstance(result, dict)
assert "output" in result
locations = sorted([element["location"] for element in result["output"]])
assert (
locations[0].endswith("output.txt")
and locations[1].endswith("output.txt_2")
and locations[2].endswith("output.txt_3")
), "Locations {} do not end with {}".format(locations, output_names)
def test_repo2cwl(self):
output_dir = tempfile.mkdtemp()
print(f'output directory:\t{output_dir}')
repo2cwl = pkg_resources.load_entry_point('ipython2cwl',
'console_scripts',
'jupyter-repo2cwl')
self.assertEqual(0, repo2cwl(['-o', output_dir, self.repo_like_dir]))
self.assertListEqual(
['example1.cwl'],
[f for f in os.listdir(output_dir) if not f.startswith('.')])
with open(os.path.join(output_dir, 'example1.cwl')) as f:
print('workflow file')
print(20 * '=')
print(f.read())
print(20 * '=')
runtime_context = RuntimeContext()
runtime_context.outdir = output_dir
runtime_context.basedir = output_dir
runtime_context.default_stdout = DEVNULL
runtime_context.default_stderr = DEVNULL
fac = cwltool.factory.Factory(runtime_context=runtime_context)
example1_tool = fac.make(os.path.join(output_dir, 'example1.cwl'))
result = example1_tool(datafilename={
'class':
'File',
'location':
os.path.join(self.repo_like_dir, 'data.yaml')
},
messages=["hello", "test", "!!!"])
with open(result['results_filename']['location'][7:]) as f:
new_data = yaml.safe_load(f)
self.assertDictEqual({
'entry1': 2,
'entry2': 'foo',
'entry3': 'bar'
}, new_data)
with open(result['messages_outputs']['location'][7:]) as f:
message = f.read()
self.assertEqual("hello test !!!", message)
shutil.rmtree(output_dir)