def test_param_get(self, pipeline_settings):
internal_raw = pipeline_settings["otu_processing"]
internal = ParamsSet(internal_raw)
curr_param = internal["otu_processing.filter.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_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.demultiplex_illumina"]
curr_param.update_location("sequence_16s",
location="file_path",
category="input")
assert external[
"otu_assignment.sequence_processing.demultiplex_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.demultiplex_454"]
user_settings = example_pipelines[
"otu_assignment_sequence_processing_demultiplex_454"]
curr_param.merge(user_settings["otu_assignment"]["sequence_processing"]
["demultiplex_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.demultiplex_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_with_pvalue",
):
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
def test_init(self, pipeline_settings):
internal_raw = pipeline_settings["otu_processing"]
assert ParamsSet(internal_raw)
wrong_format = {
"env":
"micone",
"root_dir":
"filter/partition",
"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.filter.partition", wrong_format))
with pytest.raises(TypeError):
Params((
"otu_processing.filter.partition",
{
**wrong_format, "input": "string"
},
))
with pytest.raises(TypeError):
Params((
"otu_processing.filter.partition",
{
**wrong_format, "output": "string"
},
))
with pytest.raises(TypeError):
Params((
"otu_processing.filter.partition",
{
**wrong_format, "parameters": "string"
},
))
with pytest.raises(ValueError):
Params((
"otu_processing.filter.partition",
{
**wrong_format, "input": [{
"datatype": "sequence_16s"
}]
},
))
with pytest.raises(ValueError):
Params((
"otu_processing.filter.partition",
{
**wrong_format, "output": [{
"datatype": "sequence_16s"
}]
},
))
with pytest.raises(ValueError):
Params((
"otu_processing.filter.partition",
{
**wrong_format, "parameters": [{
"data": "temp"
}]
},
))