def test_param_get(self, pipeline_settings):
internal_raw = pipeline_settings["otu_processing"]
internal = ParamsSet(internal_raw)
curr_param = internal["otu_processing.filtering.group"]
assert curr_param.get("otu_table", category="input")
assert curr_param.get("group", category="parameters")
assert curr_param.get("children_map", category="output")
def test_contains_getitem(self, pipeline_settings):
external_raw = pipeline_settings["otu_assignment"]
external = ParamsSet(external_raw)
for l1 in external_raw:
for l2 in external_raw[l1]:
for l3 in external_raw[l1][l2]:
test_external_key = f"{l1}.{l2}.{l3}"
assert test_external_key in external
def test_init(self, pipeline_settings):
internal_raw = pipeline_settings["otu_processing"]
assert ParamsSet(internal_raw)
wrong_format = {
"env": "mindpipe",
"output_location": "split_otu_table",
"input": [{"datatype": "sequence_16s", "format": ["fasta"]}],
"output": [
{"datatype": "otu_table", "format": ["biom"], "location": "*.biom"}
],
"parameters": [{"process": "something", "data": 123}],
}
assert Params(("otu_processing.filtering.partition", wrong_format))
with pytest.raises(TypeError):
Params(
(
"otu_processing.filtering.partition",
{**wrong_format, "input": "string"},
)
)
with pytest.raises(TypeError):
Params(
(
"otu_processing.filtering.partition",
{**wrong_format, "output": "string"},
)
)
with pytest.raises(TypeError):
Params(
(
"otu_processing.filtering.partition",
{**wrong_format, "parameters": "string"},
)
)
with pytest.raises(ValueError):
Params(
(
"otu_processing.filtering.partition",
{**wrong_format, "input": [{"datatype": "sequence_16s"}]},
)
)
with pytest.raises(ValueError):
Params(
(
"otu_processing.filtering.partition",
{**wrong_format, "output": [{"datatype": "sequence_16s"}]},
)
)
with pytest.raises(ValueError):
Params(
(
"otu_processing.filtering.partition",
{**wrong_format, "parameters": [{"data": "temp"}]},
)
)
def test_iter_len(self, pipeline_settings):
external_raw = pipeline_settings["otu_assignment"]
external = ParamsSet(external_raw)
count = 0
for l1 in external_raw:
for l2 in external_raw[l1]:
for l3 in external_raw[l1][l2]:
count += 1
assert count == len(external)
for process in external:
assert isinstance(process, Params)
def test_param_update_location(self, pipeline_settings):
external_raw = pipeline_settings["otu_assignment"]
external = ParamsSet(external_raw)
curr_param = external[
"otu_assignment.sequence_processing.demultiplexing_illumina"
]
curr_param.update_location(
"sequence_16s", location="file_path", category="input"
)
assert external[
"otu_assignment.sequence_processing.demultiplexing_illumina"
].get("sequence_16s", "input").location == pathlib.Path("file_path")
def test_param_merge(self, pipeline_settings, example_pipelines):
external_raw = pipeline_settings["otu_assignment"]
external = ParamsSet(external_raw)
curr_param = external["otu_assignment.sequence_processing.demultiplexing_454"]
user_settings = example_pipelines[
"otu_assignment_sequence_processing_demultiplexing_454"
]
curr_param.merge(
user_settings["otu_assignment"]["sequence_processing"]["demultiplexing_454"]
)
assert curr_param.get("sequence_16s", "input").location == pathlib.Path(
"/path/to/sequence_16s"
)
assert curr_param.get("quality", "input").location == pathlib.Path(
"/path/to/quality"
)
assert curr_param.get(
"sample_barcode_mapping", "input"
).location == pathlib.Path("/path/to/mapping")
def setup_external(
pipeline_settings,
example_pipelines,
module="otu_assignment",
pipeline="otu_assignment.sequence_processing.demultiplexing_454",
):
external_raw = pipeline_settings[module]
external = ParamsSet(external_raw)
if "." in pipeline:
pipeline_fname = pipeline.replace(".", "_")
else:
pipeline_fname = pipeline
user_settings = example_pipelines[pipeline_fname]
params = external[pipeline]
if "." in pipeline:
levels = pipeline.split(".")
x = user_settings
for i in range(len(levels)):
x = x[levels[i]]
params.merge(x)
else:
params.merge(user_settings[pipeline])
return params
def setup_internal(
pipeline_settings,
example_pipelines,
module="network_inference",
pipeline="network_inference.network.make_network",
):
internal_raw = pipeline_settings[module]
internal = ParamsSet(internal_raw)
if "." in pipeline:
pipeline_fname = pipeline.replace(".", "_")
else:
pipeline_fname = pipeline
user_settings = example_pipelines[pipeline_fname]
params = internal[pipeline]
if "." in pipeline:
levels = pipeline.split(".")
x = user_settings
for i in range(len(levels)):
x = x[levels[i]]
params.merge(x)
else:
params.merge(user_settings[pipeline])
return params