def test_substitution_without_id():
"""Test that trying to substitute links if uids haven't been assigned throws an error."""
mat = MaterialRun("A material with no id")
meas = MeasurementRun("A measurement with no id", material=mat)
with pytest.raises(ValueError):
substitute_links(
meas
), "subbed = substitute_links should fail if objects don't have uids"
with pytest.raises(ValueError):
substitute_links([meas, mat]), \
"subbed = substitute_links should fail if objects don't have uids"
with pytest.raises(ValueError):
substitute_links(meas.as_dict()), \
"subbed = substitute_links should fail if objects don't have uids"
# Create a dictionary in which either the key or value is missing a uid
meas.add_uid('id', str(uuid4()))
with pytest.raises(ValueError):
substitute_links({mat: meas}), \
"subbed = substitute_links should fail if objects don't have uids"
with pytest.raises(ValueError):
substitute_links({meas: mat}), \
"subbed = substitute_links should fail if objects don't have uids"
def ingest_material_run(data, material_spec=None, process_run=None):
"""Ingest material run with data, a material spec, and an originating process run."""
if isinstance(data, list):
return [ingest_material_run(x, material_spec) for x in data]
if not isinstance(data, dict):
raise ValueError("This ingester operates on dict, but got {}".format(type(data)))
material = MaterialRun()
sample_id = data.get("sample_id")
if sample_id:
material.add_uid("given_sample_id", sample_id)
tags = data.get("tags")
if tags:
material.tags = tags
for experiment in data.get("experiments", []):
measurement = MeasurementRun()
for name in set(known_properties.keys()).intersection(experiment.keys()):
prop = Property(
name=name,
template=known_properties[name],
value=_parse_value(experiment[name])
)
measurement.properties.append(prop)
for name in set(known_conditions.keys()).intersection(experiment.keys()):
cond = Condition(
name=name,
template=known_conditions[name],
value=_parse_value(experiment[name])
)
measurement.conditions.append(cond)
for name in set(known_parameters.keys()).intersection(experiment.keys()):
param = Parameter(
name=name,
template=known_parameters[name],
value=_parse_value(experiment[name])
)
measurement.parameters.append(param)
scan_id = experiment.get("scan_id")
if scan_id:
measurement.add_uid("given_scan_id", scan_id)
tags = experiment.get("tags")
if tags:
measurement.tags = tags
measurement.material = material
if material_spec:
material.material_spec = material_spec
if process_run:
material.process = process_run
return material