def test_repr(self):
try:
unicode
except NameError:
cell = PatchedCell("example001",
brain_location=BrainRegion("primary auditory cortex"),
collection=None,
cell_type=CellType("pyramidal cell"),
experiments=None,
pipette_id=31,
seal_resistance=QuantitativeValue(1.2, "GΩ"),
pipette_resistance=QuantitativeValue(1.5, "MΩ"),
liquid_junction_potential=None,
labeling_compound="0.1% biocytin ",
reversal_potential_cl=None)
expected_repr = ("PatchedCell(name='example001', "
"brain_location=BrainRegion('primary auditory cortex', 'http://purl.obolibrary.org/obo/UBERON_0034751'), "
"cell_type=CellType('pyramidal cell', 'http://purl.obolibrary.org/obo/CL_0000598'), "
"pipette_id=31, seal_resistance=QuantitativeValue(1.2 'GΩ'), "
"pipette_resistance=QuantitativeValue(1.5 'MΩ'), "
"labeling_compound='0.1% biocytin ', id=None)")
assert repr(cell) == expected_repr
else:
pytest.skip(
"The remaining lifespan of Python 2 is too short to fix unicode representation errors")
def generate_random_object(cls, all_fields=True):
attrs = {}
for field in cls.fields:
if all_fields or field.required:
obj_type = field.types[
0] # todo: pick randomly if len(field.types) > 1
if not field.intrinsic:
value = None
elif obj_type == basestring:
value = _random_text()
elif obj_type == int:
value = random.randint(1, 10)
elif obj_type == float:
value = random.uniform(0, 1000)
elif issubclass(obj_type, KGObject):
if obj_type == KGObject:
# specific type is not determined
# arbitrarily, let's choose minds.Dataset
value = MockKGObject(id=random_uuid(),
type=["minds:Dataset"])
else:
value = MockKGObject(id=random_uuid(),
type=getattr(obj_type, "type", None))
elif obj_type == QuantitativeValue:
# todo: subclass QV so we can specify the required dimensionality in `fields`
value = QuantitativeValue(
random.uniform(-10, 10),
random.choice(list(QuantitativeValue.unit_codes)))
elif obj_type == QuantitativeValueRange:
# todo: subclass QVR so we can specify the required dimensionality in `fields`
min = random.uniform(-10, 10)
value = QuantitativeValueRange(
min, min + random.uniform(1, 10),
random.choice(list(QuantitativeValue.unit_codes)))
elif issubclass(obj_type, OntologyTerm):
value = obj_type(random.choice(list(obj_type.iri_map)))
elif obj_type == datetime:
value = datetime.now()
elif obj_type == date:
value = date.today()
elif obj_type == bool:
value = random.choice([True, False])
elif obj_type == Distribution:
value = Distribution("http://example.com/myfile.txt")
elif obj_type == Age:
value = Age(QuantitativeValue(random.randint(7, 150), "days"),
"Post-natal")
elif obj_type == IRI:
value = "http://example.com/åêïøù"
elif obj_type == Address:
value = Address("Paris", "France")
elif obj_type == dict:
value = {"a": 1, "b": 2}
else:
raise NotImplementedError(str(obj_type))
attrs[field.name] = value
return cls(**attrs)
def test_round_trip(self, kg_client):
trace1 = Trace("example001",
data_location=Distribution(
"http://example.com/example.csv",
content_type="text/tab-separated-values"),
generated_by=MockKGObject(
id="http://fake_uuid_abc123",
type=PatchClampExperiment.type),
generation_metadata=MockKGObject(
id="http://fake_uuid_def456",
type=QualifiedTraceGeneration.type),
channel=42,
data_unit="mV",
time_step=QuantitativeValue(0.1, "ms"),
part_of=MockKGObject(id="http://fake_uuid_ghi789",
type=Dataset.type))
instance = Instance(Trace.path, trace1._build_data(kg_client),
Instance.path)
instance.data["@id"] = "http://fake_uuid_6a5d6ecf87"
instance.data["@type"] = Trace.type
trace2 = Trace.from_kg_instance(instance, kg_client)
for field in ("name", "data_location", "channel", "data_unit",
"time_step"):
assert getattr(trace1, field) == getattr(trace2, field)
for field in ("generated_by", "generation_metadata", "part_of"):
obj1 = getattr(trace1, field)
obj2 = getattr(trace2, field)
assert isinstance(obj2, KGProxy)
assert obj1.id == obj2.id
assert obj1.type == obj2.type
def test_from_jsonld_alt(self):
data = {
"http://schema.org/value": 0.05,
"http://schema.org/unitText": "ms"
}
obj = QuantitativeValue.from_jsonld(data)
assert obj.value == 0.05
assert obj.unit_text == "ms"
def test_round_trip(self, kg_client):
obj1 = Subject(name="Mickey", species=Species("Mus musculus"),
strain=Strain("129/Sv"), sex=Sex("male"),
age=Age(QuantitativeValue(20, "days"), "Post-natal"),
death_date=datetime(1960, 1, 1))
instance = Instance(Subject.path, obj1._build_data(kg_client), Instance.path)
instance.data["@id"] = "http://fake_uuid_9ab2227fe1"
instance.data["@type"] = Subject.type
obj2 = Subject.from_kg_instance(instance, kg_client)
for field in ("name", "species", "strain", "sex", "age", "death_date"):
assert getattr(obj1, field) == getattr(obj2, field)
def test_round_trip(self, kg_client):
cell1 = PatchedCell("example001",
brain_location=BrainRegion("primary auditory cortex"),
collection=None,
cell_type=CellType("pyramidal cell"),
experiments=None,
pipette_id=31,
seal_resistance=QuantitativeValue(1.2, "GΩ"),
pipette_resistance=QuantitativeValue(1.5, "MΩ"),
liquid_junction_potential=QuantitativeValue(5.0, "mV"),
labeling_compound="0.1% biocytin ",
reversal_potential_cl=QuantitativeValue(-65, "mV"))
instance = Instance(PatchedCell.path, cell1._build_data(kg_client), Instance.path)
instance.data["@id"] = "http://fake_uuid_93f9cd9a9b"
instance.data["@type"] = PatchedCell.type
cell2 = PatchedCell.from_kg_instance(instance, kg_client)
for field in ("name", "brain_location", "cell_type",
"pipette_id", "seal_resistance", "pipette_resistance",
"liquid_junction_potential", "labeling_compound",
"reversal_potential_cl"):
assert getattr(cell1, field) == getattr(cell2, field)
def test_repr(self):
cell = PatchedCell(
"example001",
brain_location=BrainRegion("primary auditory cortex"),
collection=None,
cell_type=CellType("pyramidal cell"),
experiments=None,
pipette_id=31,
seal_resistance=QuantitativeValue(1.2, "GΩ"),
pipette_resistance=QuantitativeValue(1.5, "MΩ"),
liquid_junction_potential=None,
labeling_compound="0.1% biocytin ",
reversal_potential_cl=None)
expected_repr = (
"PatchedCell(name='example001', "
"brain_location=BrainRegion('primary auditory cortex', 'http://uri.interlex.org/ilx_0443027'), "
"cell_type=CellType('pyramidal cell', 'http://uri.interlex.org/ilx_0107385'), "
"pipette_id=31, seal_resistance=QuantitativeValue(1.2 'GΩ'), "
"pipette_resistance=QuantitativeValue(1.5 'MΩ'), "
"labeling_compound='0.1% biocytin ', id=None)")
assert repr(cell) == expected_repr
def test_list_nexus(self, kg_client):
cells = PatchedCell.list(kg_client, api="nexus", size=50)
assert len(cells) == 30
assert cells[0].brain_location == BrainRegion("hippocampus CA1")
assert isinstance(cells[0].collection, KGQuery)
assert cells[0].cell_type == CellType("hippocampus CA1 pyramidal cell")
assert isinstance(cells[0].experiments, KGQuery)
assert cells[0].pipette_id is None
assert cells[0].seal_resistance is None
assert cells[0].pipette_resistance is None
assert cells[0].liquid_junction_potential is None
assert cells[0].labeling_compound is None
assert cells[0].reversal_potential_cl == QuantitativeValue(-16.0, unit_text="mV")