def test_build_bad(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(pipeline_settings, example_pipelines)
process = Process(params, profile="local")
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")
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_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_build_good(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filtering.group",
)
process = Process(params, profile="local")
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.filtering.group.nf")
config_file = os.path.join(process_dir, "otu_processing.filtering.group.config")
assert os.path.exists(script_file)
assert os.path.exists(config_file)
def test_dict(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filtering.group",
)
process = Process(params, profile="local")
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)
param_dict = process.params.dict
assert "input" in param_dict
assert "output" in param_dict
assert "output_dir" in param_dict
for params in process.params.parameters:
assert params.process in param_dict
def test_cmd(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filtering.group",
)
process = Process(params, profile="local")
with pytest.warns(UserWarning):
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")
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", "pvalue_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")
json_process = Process(json_params, profile="local")
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")
curr_params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filtering.group",
)
curr_process = Process(curr_params, profile="local")
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()
def test_clean(self, pipeline_settings, example_pipelines, tmpdir):
params = setup_internal(
pipeline_settings,
example_pipelines,
module="otu_processing",
pipeline="otu_processing.filtering.group",
)
process = Process(params, profile="local")
process_dir = tmpdir.mkdir("test_process_clean")
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]
process.run()
process.wait()
for path in paths:
assert pathlib.Path(path).exists()
process.clean("all")
for path in paths:
assert not pathlib.Path(path).exists()
process.build(process_dir)
process.clean("work_dir")
for path in paths:
if "work" in path:
assert not pathlib.Path(path).exists()
else:
if not path.endswith(".log"):
assert pathlib.Path(path).exists()