def test_build_bad(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(pipeline_settings, example_pipelines)
process = Process(params, profile="local", output_location=".")
process_dir = tmpdir.mkdir("test_process_build")
output_dir = pathlib.Path.cwd() / "tests/data"
with pytest.raises(FileNotFoundError):
process.build(process_dir)
process.update_location(str(output_dir), "input")
process.build(process_dir)
def test_run(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_external(
pipeline_settings,
example_pipelines,
module="network_inference",
pipeline="network_inference.correlation.sparcc",
)
process = Process(params, profile="local", output_location=".")
process_dir = tmpdir.mkdir("test_process_run")
output_dir = pathlib.Path.cwd() / "tests/data"
process.update_location(str(output_dir), "input")
process.build(process_dir)
process.run()
assert process.output
assert not process.error
process.log()
for output in process.params.output:
if "*" in str(output.location):
str_loc = str(output.location)
ind = str_loc.find("*")
files = list(pathlib.Path(str_loc[:ind]).glob(str_loc[ind:]))
assert len(files) > 0
else:
assert output.location.exists()
def test_update_location(self, pipeline_settings, example_pipelines):
params = setup_internal(pipeline_settings, example_pipelines)
process = Process(params, profile="local", output_location=".")
output_dir = pathlib.Path.home() / "Documents/results"
process.update_location(str(output_dir), "input")
for input_ in process.params.input:
assert str(input_.location).startswith(str(pathlib.Path.home()))
for output_ in process.params.output:
assert not output_.location.is_absolute()
process.update_location(str(output_dir), "output")
for output_ in process.params.output:
assert str(output_.location).startswith(str(pathlib.Path.home()))
def test_dict(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filter.group",
)
process = Process(params, profile="local", output_location=".")
process_dir = tmpdir.mkdir("test_process_dict")
output_dir = pathlib.Path.cwd() / "tests/data"
process.update_location(str(output_dir), "input")
process.build(process_dir)
assert process.params.input
assert process.params.output
assert process.params.root_dir
for params in process.params.parameters:
assert params.process in params
def test_build_good(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filter.group",
)
process = Process(params, profile="local", output_location=".")
process_dir = tmpdir.mkdir("test_process_build")
output_dir = pathlib.Path.cwd() / "tests/data"
process.update_location(str(output_dir), "input")
process.build(process_dir)
script_file = os.path.join(process_dir,
"otu_processing.filter.group.nf")
config_file = os.path.join(process_dir,
"otu_processing.filter.group.config")
assert os.path.exists(script_file)
assert os.path.exists(config_file)
def test_cmd(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filter.group",
)
process = Process(params, profile="local", output_location=".")
assert process.cmd
process_dir = tmpdir.mkdir("test_process_cmd")
output_dir = pathlib.Path.cwd() / "tests/data"
process.update_location(str(output_dir), "input")
process.build(process_dir)
cmd = process.cmd
paths = [
p for p in str(cmd).split(" ")
if not p.startswith("-") and "/" in p
]
for path in paths:
if path.endswith(".config") or path.endswith(".nf"):
assert pathlib.Path(path).exists()
def test_init(self, pipeline_settings, example_pipelines):
params = setup_internal(pipeline_settings, example_pipelines)
assert Process(params, profile="local", output_location=".")
def test_ix_attach_to(self, pipeline_settings, example_pipelines, tmpdir):
sparcc_params = setup_external(
pipeline_settings,
example_pipelines,
module="network_inference",
pipeline="network_inference.correlation.sparcc",
)
json_params = setup_internal(pipeline_settings, example_pipelines)
to_remove = []
for io_elem in json_params.input:
if io_elem.datatype in {"interaction_table"}:
to_remove.append(io_elem)
for remove in to_remove:
json_params.input.remove(remove)
json_params.input.add(
Input(datatype=remove.datatype, format=remove.format))
sparcc_process = Process(sparcc_params,
profile="local",
output_location=".")
json_process = Process(json_params,
profile="local",
output_location=".")
output_dir = pathlib.Path.cwd() / "tests/data"
sparcc_process.update_location(str(output_dir), "input")
sparcc_process.build(tmpdir)
json_process.attach_to(sparcc_process)
json_process.update_location(str(output_dir), "input")
with pytest.raises(FileNotFoundError):
json_process.build(tmpdir)
sparcc_process.run()
sparcc_process.wait()
json_process.build(tmpdir)
json_process.run()
json_process.wait()
def test_attach_to(self, pipeline_settings, example_pipelines, tmpdir):
previous_params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.transform.normalize",
)
previous_process = Process(previous_params,
profile="local",
output_location=".")
curr_params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filter.group",
)
curr_process = Process(curr_params,
profile="local",
output_location=".")
output_dir = pathlib.Path.cwd() / "tests/data"
previous_process.update_location(str(output_dir), "input")
previous_process.build(tmpdir)
curr_process.attach_to(previous_process)
with pytest.raises(FileNotFoundError):
curr_process.build(tmpdir)
previous_process.run()
previous_process.output
curr_process.update_location(str(output_dir), "input")
curr_process.build(tmpdir)
curr_process.run()