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()