def test_material_spec():
"""Test that Process/Material Spec link survives serialization."""
# Create a ProcessSpec
proc_spec = ProcessSpec(name="a process spec", tags=["tag1", "tag2"])
# Create MaterialSpec without a ProcessSpec
prop = Property(name="The material is a solid",
value=DiscreteCategorical(probabilities="solid"))
mat_spec = MaterialSpec(name="a material spec",
properties=PropertyAndConditions(prop))
assert mat_spec.process is None, \
"MaterialSpec should be initialized with no ProcessSpec, by default"
# Assign a ProcessSpec to mat_spec, first ensuring that the type is enforced
with pytest.raises(TypeError):
mat_spec.process = 17
mat_spec.process = proc_spec
# Assert circular links
assert dumps(proc_spec.output_material.process) == dumps(proc_spec), \
"ProcessSpec should link to MaterialSpec that links back to itself"
assert dumps(mat_spec.process.output_material) == dumps(mat_spec), \
"MaterialSpec should link to ProcessSpec that links back to itself"
# Make copies of both specs
mat_spec_copy = loads(dumps(mat_spec))
proc_spec_copy = loads(dumps(proc_spec))
assert proc_spec_copy.output_material == mat_spec, \
"Serialization should preserve link from ProcessSpec to MaterialSpec"
assert mat_spec_copy.process == proc_spec, \
"Serialization should preserve link from MaterialSpec to ProcessSpec"
def test_process_reassignment():
"""Test that a material can be assigned to a new process."""
drying = ProcessSpec("drying")
welding = ProcessSpec("welding")
powder = MaterialSpec("Powder", process=welding)
assert powder.process == welding
assert welding.output_material == powder
powder.process = drying
assert powder.process == drying
assert drying.output_material == powder
assert welding.output_material is None
def test_circular_crawl():
"""Test that make_instance can handle a circular set of linked objects."""
proc = ProcessSpec("process name")
mat = MaterialSpec("material name", process=proc)
IngredientSpec(name="ingredient name", material=mat, process=proc)
mat_run = make_instance(mat)
assert mat_run == mat_run.process.ingredients[0].material
def test_serialized_history():
"""Test the serialization of a complete material history."""
# Create several runs and specs linked together
buy_spec = LinkByUID("id", "pr723")
cookie_dough_spec = MaterialSpec("cookie dough spec", process=buy_spec)
buy_cookie_dough = ProcessRun("Buy cookie dough", uids={'id': '32283'}, spec=buy_spec)
cookie_dough = MaterialRun("cookie dough", process=buy_cookie_dough, spec=cookie_dough_spec)
bake = ProcessRun("bake cookie dough", conditions=[
Condition("oven temp", origin='measured', value=NominalReal(357, 'degF'))])
IngredientRun(material=cookie_dough,
process=bake, number_fraction=NominalReal(1, ''))
cookie = MaterialRun("cookie", process=bake, tags=["chocolate chip", "drop"])
MeasurementRun("taste", material=cookie, properties=[
Property("taste", value=DiscreteCategorical("scrumptious"))])
cookie_history = complete_material_history(cookie)
# There are 7 entities in the serialized list: cookie dough (spec & run), buy cookie dough,
# cookie dough ingredient, bake cookie dough, cookie, taste
assert len(cookie_history) == 7
for entity in cookie_history:
assert len(entity['uids']) > 0, "Serializing material history should assign uids."
# Check that the measurement points to the material
taste_dict = next(x for x in cookie_history if x.get('type') == 'measurement_run')
cookie_dict = next(x for x in cookie_history if x.get('name') == 'cookie')
scope = taste_dict.get('material').get('scope')
assert taste_dict.get('material').get('id') == cookie_dict.get('uids').get(scope)
# Check that both the material spec and the process run point to the same process spec.
# Because that spec was initially a LinkByUID, this also tests the methods ability to
# serialize a LinkByUID.
cookie_dough_spec_dict = next(x for x in cookie_history if x.get('type') == 'material_spec')
buy_cookie_dough_dict = next(x for x in cookie_history if x.get('name') == 'Buy cookie dough')
assert cookie_dough_spec_dict.get('process') == buy_spec.as_dict()
assert buy_cookie_dough_dict.get('spec') == buy_spec.as_dict()
def __init__(self,
name: str,
*,
uids: Optional[Dict[str, str]] = None,
tags: Optional[List[str]] = None,
notes: Optional[str] = None,
process: Optional[GEMDProcessSpec] = None,
properties: Optional[List[PropertyAndConditions]] = None,
template: Optional[GEMDMaterialTemplate] = None,
file_links: Optional[List[FileLink]] = None):
if uids is None:
uids = dict()
DataConcepts.__init__(self, GEMDMaterialSpec.typ)
GEMDMaterialSpec.__init__(self, name=name, uids=uids,
tags=tags, process=process, properties=properties,
template=template, file_links=file_links, notes=notes)
def test_make_instance():
"""Build up several linked objects and test their properties."""
msr_spec = MeasurementSpec()
assert isinstance(make_instance(msr_spec), MeasurementRun)
mat_spec = MaterialSpec(name='Mat name')
mat_spec.process = ProcessSpec(name='Pro name')
IngredientSpec(name='Ing label', process=mat_spec.process)
mat_spec.process.ingredients[0].material = MaterialSpec(name='Baby mat name')
mat_run = make_instance(mat_spec)
assert isinstance(mat_run, MaterialRun)
assert isinstance(mat_run.process, ProcessRun)
assert isinstance(mat_run.process.ingredients[0], IngredientRun)
assert isinstance(mat_run.process.ingredients[0].material, MaterialRun)
assert mat_run.process.spec == mat_run.spec.process
ingredient = mat_run.process.ingredients[0]
assert ingredient.spec == mat_run.spec.process.ingredients[0]
assert ingredient.material.spec == mat_run.spec.process.ingredients[0].material
def test_ingredient_spec():
"""Tests that a process can house an ingredient, and that pairing survives serialization."""
# Create a ProcessSpec
proc_spec = ProcessSpec(name="a process spec", tags=["tag1", "tag2"])
IngredientSpec(name='Input',
material=MaterialSpec(name='Raw'),
process=proc_spec)
# Make copies of both specs
proc_spec_copy = loads(dumps(proc_spec))
assert proc_spec_copy == proc_spec, "Full structure wasn't preserved across serialization"
def make_strehlow_objects(table=None, template_scope=DEMO_TEMPLATE_SCOPE):
"""Make a table with Strehlow & Cook data."""
tmpl = make_templates(template_scope)
if table is None:
table = import_table()
# Specs
msr_spec = MeasurementSpec(name='Band gap',
template=tmpl["Band gap measurement"]
)
def real_mapper(prop):
"""Mapping methods for RealBounds."""
if 'uncertainty' in prop['scalars'][0]:
if prop['units'] == 'eV': # Arbitrarily convert to attojoules
mean = convert_units(value=float(prop['scalars'][0]['value']),
starting_unit=prop['units'],
final_unit='aJ'
)
std = convert_units(value=float(prop['scalars'][0]['value']),
starting_unit=prop['units'],
final_unit='aJ'
)
val = NormalReal(mean=mean,
units='aJ',
std=std
)
else:
val = NormalReal(mean=float(prop['scalars'][0]['value']),
units=prop['units'],
std=float(prop['scalars'][0]['uncertainty'])
)
else:
val = NominalReal(nominal=float(prop['scalars'][0]['value']),
units=prop['units']
)
return val
content_map = {
RealBounds: real_mapper,
CategoricalBounds: lambda prop: NominalCategorical(category=prop['scalars'][0]['value']),
type(None): lambda bnd: 'Label'
}
datapoints = []
compounds = dict()
for row in table:
formula = formula_clean(row['chemicalFormula'])
if formula not in compounds:
compounds[formula] = MaterialSpec(
name=formula_latex(formula),
template=tmpl["Chemical"],
process=ProcessSpec(name="Sample preparation",
template=tmpl["Sample preparation"]
))
spec = compounds[formula]
run = make_instance(spec)
datapoints.append(run)
if not spec.properties:
spec.properties.append(
PropertyAndConditions(
property=Property(name=spec.template.properties[0][0].name,
value=EmpiricalFormula(formula=formula),
template=spec.template.properties[0][0])
))
msr = make_instance(msr_spec)
msr.material = run
# 2 categories in the PIF need to be split to avoid repeat Attribute Templates in a Run
name_map = {
'Phase': 'Crystal system',
'Transition': 'Bands'
}
origin_map = {
'EXPERIMENTAL': Origin.MEASURED,
'COMPUTATIONAL': Origin.COMPUTED
}
seen = set() # Some conditions come in from multiple properties on the same object
for prop in row['properties']:
origin = origin_map.get(prop.get('dataType', None), Origin.UNKNOWN)
if 'method' in prop:
method = 'Method: ' + prop['method']['name']
else:
method = 'Method: unreported'
for attr in [prop] + prop.get('conditions', []):
if attr['name'] in seen:
# Early return if it's a repeat
continue
seen.add(attr['name'])
template = tmpl[attr['name']]
# Figure out if we need to split this column
if attr['name'] in name_map:
value = attr['scalars'][0]['value']
if value not in template.bounds.categories:
template = tmpl[name_map[attr['name']]]
# Move into GEMD structure
if type(template) == PropertyTemplate:
msr.properties.append(
Property(name=template.name,
template=template,
value=content_map[type(template.bounds)](attr),
origin=origin,
notes=method
))
elif type(template) == ConditionTemplate:
msr.conditions.append(
Condition(name=template.name,
template=template,
value=content_map[type(template.bounds)](attr),
origin=origin,
notes=method
))
return datapoints
def test_invalid_assignment():
"""Invalid assignments to `process` or `template` throw a TypeError."""
with pytest.raises(TypeError):
MaterialSpec("name", process=["Process 1", "Process 2"])
with pytest.raises(TypeError):
MaterialSpec("name", template=MaterialSpec("another spec"))