def test_serialize():
"""Serializing a nested object should be identical to individually serializing each piece."""
condition = Condition(name="A condition", value=NominalReal(7, ''))
parameter = Parameter(name="A parameter",
value=NormalReal(mean=17, std=1, units=''))
input_material = MaterialRun(tags="input")
process = ProcessRun(tags="A tag on a process run")
ingredient = IngredientRun(material=input_material, process=process)
material = MaterialRun(tags=["A tag on a material"], process=process)
measurement = MeasurementRun(tags="A tag on a measurement",
conditions=condition,
parameters=parameter,
material=material)
# serialize the root of the tree
native_object = json.loads(dumps(measurement))
# ingredients don't get serialized on the process
assert (len(native_object["context"]) == 5)
assert (native_object["object"]["type"] == LinkByUID.typ)
# serialize all of the nodes
native_batch = json.loads(
dumps([material, process, measurement, ingredient]))
assert (len(native_batch["context"]) == 5)
assert (len(native_batch["object"]) == 4)
assert (all(x["type"] == LinkByUID.typ for x in native_batch["object"]))
def test_material_run():
"""
Test the ability to create a MaterialRun that is linked to a MaterialSpec.
Make sure all enumerated values are respected, and check consistency after
serializing and deserializing.
"""
# Define a property, and make sure that an inappropriate value for origin throws ValueError
with pytest.raises(ValueError):
prop = Property(name="A property", origin="bad origin", value=NominalReal(17, units=''))
# Create a MaterialSpec with a property
prop = Property(name="A property", origin="specified", value=NominalReal(17, units=''))
mat_spec = MaterialSpec(
name="a specification for a material",
properties=PropertyAndConditions(prop),
notes="Funny lookin'"
)
# Make sure that when property is serialized, origin (an enumeration) is serialized as a string
copy_prop = json.loads(dumps(mat_spec))
copy_origin = copy_prop["context"][0]["properties"][0]['property']['origin']
assert isinstance(copy_origin, str)
# Create a MaterialRun, and make sure an inappropriate value for sample_type throws ValueError
with pytest.raises(ValueError):
mat = MaterialRun("name", spec=mat_spec, sample_type="imaginary")
mat = MaterialRun("name", spec=mat_spec, sample_type="virtual")
# ensure that serialization does not change the MaterialRun
copy = loads(dumps(mat))
assert dumps(copy) == dumps(mat), \
"Material run is modified by serialization or deserialization"
def test_complex_substitutions():
"""Make sure accounting works for realistic objects."""
root = MaterialRun("root",
process=ProcessRun("root", spec=ProcessSpec("root")),
spec=MaterialSpec("root"))
root.spec.process = root.process.spec
input = MaterialRun("input",
process=ProcessRun("input", spec=ProcessSpec("input")),
spec=MaterialSpec("input"))
input.spec.process = input.process.spec
IngredientRun(process=root.process,
material=input,
spec=IngredientSpec("ingredient",
process=root.process.spec,
material=input.spec))
param = ParameterTemplate("Param", bounds=RealBounds(-1, 1, "m"))
root.process.spec.template = ProcessTemplate("Proc", parameters=[param])
root.process.parameters.append(
Parameter("Param", value=NormalReal(0, 1, 'm'), template=param))
links = flatten(root, scope="test-scope")
index = make_index(links)
rebuild = substitute_objects(links, index, inplace=True)
rebuilt_root = next(x for x in rebuild
if x.name == root.name and x.typ == root.typ)
all_objs = recursive_flatmap(rebuilt_root,
func=lambda x: [x],
unidirectional=False)
unique = [x for i, x in enumerate(all_objs) if i == all_objs.index(x)]
assert not any(isinstance(x, LinkByUID) for x in unique), "All are objects"
assert len(links) == len(unique), "Objects are missing"
def test_invalid_assignment():
"""Invalid assignments to `process` or `spec` throw a TypeError."""
with pytest.raises(TypeError):
MaterialRun(name=12)
with pytest.raises(TypeError):
MaterialRun("name", spec=ProcessRun("a process"))
with pytest.raises(TypeError):
MaterialRun("name", process=MaterialSpec("a spec"))
def test_template_access():
"""A material run's template should be equal to its spec's template."""
template = MaterialTemplate("material template", uids={'id': str(uuid4())})
spec = MaterialSpec("A spec", uids={'id': str(uuid4())}, template=template)
mat = MaterialRun("A run", uids=['id', str(uuid4())], spec=spec)
assert mat.template == template
mat.spec = LinkByUID.from_entity(spec)
assert mat.template is None
def test_dependencies():
"""Test that dependency lists make sense."""
ps = ProcessSpec(name="ps")
pr = ProcessRun(name="pr", spec=ps)
ms = MaterialSpec(name="ms", process=ps)
mr = MaterialRun(name="mr", spec=ms, process=pr)
assert ps not in mr.all_dependencies()
assert pr in mr.all_dependencies()
assert ms in mr.all_dependencies()
def test_build():
"""Test that build recreates the material."""
spec = MaterialSpec("A spec",
properties=PropertyAndConditions(
property=Property("a property", value=NominalReal(3, ''))),
tags=["a tag"])
mat = MaterialRun(name="a material", spec=spec)
mat_dict = mat.as_dict()
mat_dict['spec'] = mat.spec.as_dict()
assert MaterialRun.build(mat_dict) == mat
def test_equality():
"""Test that equality check works as expected."""
spec = MaterialSpec(
"A spec",
properties=PropertyAndConditions(
property=Property("a property", value=NominalReal(3, ''))),
tags=["a tag"])
mat1 = MaterialRun("A material", spec=spec)
mat2 = MaterialRun("A material", spec=spec, tags=["A tag"])
assert mat1 == deepcopy(mat1)
assert mat1 != mat2
assert mat1 != "A material"
def test_process_reassignment():
"""Test that a material can be assigned to a new process."""
drying = ProcessRun("drying")
welding = ProcessRun("welding")
powder = MaterialRun("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_process_id_link():
"""Test that a process run can house a LinkByUID object, and that it survives serde."""
uid = str(uuid4())
proc_link = LinkByUID(scope='id', id=uid)
mat_run = MaterialRun("Another cake", process=proc_link)
copy_material = loads(dumps(mat_run))
assert dumps(copy_material) == dumps(mat_run)
def test_dict_serialization():
"""Test that a dictionary can be serialized and then deserialized as a gemd object."""
process = ProcessRun("A process")
mat = MaterialRun("A material", process=process)
meas = MeasurementRun("A measurement", material=mat)
copy = loads(dumps(meas.as_dict()))
assert copy == meas
def test_order_objects():
"""Test that sorting works when given objects."""
unsorted = [MaterialRun("bar"), ProcessRun("foo")]
sorted_list = sorted(unsorted, key=lambda x: writable_sort_order(x))
assert isinstance(sorted_list[0], ProcessRun)
assert isinstance(sorted_list[1], MaterialRun)
def test_exceptions():
"""Additional tests to get full coverage on exceptions."""
with pytest.raises(ValueError):
add_edge(MaterialRun("Input"), make_node("Output"))
with pytest.raises(ValueError):
add_edge(make_node("Input"),
MaterialRun("Output", spec=LinkByUID("Bad", "ID")))
with pytest.raises(ValueError):
add_measurement(make_node('Material'),
name='Measurement',
attributes=[UnsupportedAttribute("Spider-man")])
with pytest.raises(ValueError):
make_attribute(UnsupportedAttributeTemplate, 5)
def test_uid_deser():
"""Test that uids continue to be a CaseInsensitiveDict after deserialization."""
material = MaterialRun("Input material", tags="input", uids={'Sample ID': '500-B'})
ingredient = IngredientRun(material=material)
ingredient_copy = loads(dumps(ingredient))
assert isinstance(ingredient_copy.uids, CaseInsensitiveDict)
assert ingredient_copy.material == material
assert ingredient_copy.material.uids['sample id'] == material.uids['Sample ID']
def test_material_soft_link():
"""Test that a measurement run can link to a material run, and that it survives serde."""
dye = MaterialRun("rhodamine",
file_links=FileLink(filename='a.csv', url='/a/path'))
assert dye.measurements == [], "default value of .measurements should be an empty list"
# The .measurements member should not be settable
with pytest.raises(AttributeError):
dye.measurements = [MeasurementRun("Dummy")]
absorbance = MeasurementRun(name="Absorbance",
uids={'id': str(uuid4())},
properties=[
Property(name='Abs at 500 nm',
value=NominalReal(0.1, ''))
])
assert absorbance.material is None, "Measurements should have None as the material by default"
absorbance.material = dye
assert absorbance.material == dye, "Material not set correctly for measurement"
assert dye.measurements == [
absorbance
], "Soft-link from material to measurement not created"
fluorescence = MeasurementRun(name="Fluorescence",
uids={'id': str(uuid4())},
properties=[
Property(name='PL counts at 550 nm',
value=NominalReal(30000, ''))
],
material=dye)
assert fluorescence.material == dye, "Material not set correctly for measurement"
assert dye.measurements == [absorbance, fluorescence], \
"Soft-link from material to measurements not created"
assert loads(dumps(absorbance)) == absorbance, \
"Measurement should remain unchanged when serialized"
assert loads(dumps(fluorescence)) == fluorescence, \
"Measurement should remain unchanged when serialized"
assert 'measurements' in repr(dye)
assert 'material' in repr(fluorescence)
assert 'material' in repr(absorbance)
subbed = substitute_links(dye)
assert 'measurements' in repr(subbed)
def test_measurement_reassignment():
"""Check that a measurement run can be re-assigned to a new material run."""
sample1 = MaterialRun("Sample 1")
sample2 = MaterialRun("Sample 2")
mass = MeasurementRun("Mass of sample", material=sample1)
volume = MeasurementRun("Volume of sample", material=sample1)
assert mass.material == sample1
assert set(sample1.measurements) == {mass, volume}
assert sample2.measurements == []
mass.material = sample2
assert mass.material == sample2
assert sample1.measurements == [volume]
assert sample2.measurements == [mass]
mass.material = None
assert mass.material is None
assert sample2.measurements == []
def test_from_entity():
"""Test permutations of LinkByUID.from_entity arguments."""
run = MaterialRun(name='leaf', process=ProcessRun(name='leaf proc'))
assert LinkByUID.from_entity(run).scope == 'auto'
assert LinkByUID.from_entity(run, scope='missing').scope == 'auto'
assert len(run.uids) == 1
run.uids['foo'] = 'bar'
link1 = LinkByUID.from_entity(run, scope='foo')
assert (link1.scope, link1.id) == ('foo', 'bar')
with pytest.deprecated_call():
assert LinkByUID.from_entity(run, 'foo').scope == 'foo'
with pytest.deprecated_call():
assert LinkByUID.from_entity(run, name='foo').scope == 'foo'
with pytest.raises(ValueError):
LinkByUID.from_entity(run, name='scope1', scope='scope2')
def test_make_index():
"""Test functionality of make_index method."""
ps1 = ProcessSpec(name="hello", uids={"test_scope": "test_value"})
pr1 = ProcessRun(
name="world",
spec=LinkByUID(scope="test_scope", id="test_value"),
uids={"test_scope": "another_test_value",
"other_test": "also_valid"
},
)
ms1 = MaterialSpec(
name="material",
process=LinkByUID(scope="test_scope", id="test_value"),
uids={"second_scope": "this_is_an_id"},
)
mr1 = MaterialRun(
name="material_run",
spec=LinkByUID(scope="second_scope", id="this_is_an_id"),
process=LinkByUID(scope="test_scope", id="another_test_value"),
)
pr2 = ProcessRun(
name="goodbye",
spec=LinkByUID.from_entity(ps1),
uids={"test_scope": "the_other_value"},
)
mr2 = MaterialRun(
name="cruel",
spec=LinkByUID.from_entity(ms1),
process=LinkByUID.from_entity(pr2),
)
gems = [ps1, pr1, ms1, mr1, pr2, mr2]
gem_index = make_index(gems)
for gem in gems:
for scope in gem.uids:
assert (scope, gem.uids[scope]) in gem_index
assert gem_index[(scope, gem.uids[scope])] == gem
# Make sure substitute_objects can consume the index
subbed = substitute_objects(mr1, gem_index)
assert subbed.spec.uids == ms1.uids
def make_node(name: str,
*,
process_name: str = None,
process_template: ProcessTemplate = None,
material_template: MaterialTemplate = None) -> MaterialRun:
"""
Generate a material-process spec-run quadruple.
Parameters
----------
name: str
Name of the MaterialRun and MaterialSpec.
process_name: str
Name of the ProcessRun and ProcessSpec. Defaults to
`process_template.name` if `process_template` is defined, else `name`.
process_template: ProcessTemplate
ProcessTemplate for the quadruple.
material_template: MaterialTemplate
MaterialTemplate for the quadruple.
Returns
--------
MaterialRun
A MaterialRun with linked processes, specs and templates
"""
if process_name is None:
if process_template is None:
process_name = name
else:
process_name = process_template.name
my_process_spec = ProcessSpec(
name=process_name,
template=process_template
)
my_process_run = ProcessRun(
name=process_name,
spec=my_process_spec
)
my_mat_spec = MaterialSpec(
name=name,
process=my_process_spec,
template=material_template
)
my_mat_run = MaterialRun(
name=name,
process=my_process_run,
spec=my_mat_spec
)
return my_mat_run
def test_recursive_foreach():
"""Test that recursive foreach will actually walk through a material history."""
mat_run = MaterialRun("foo")
process_run = ProcessRun("bar")
IngredientRun(process=process_run, material=mat_run)
output = MaterialRun("material", process=process_run)
# property templates are trickier than templates because they are referenced in attributes
template = PropertyTemplate("prop", bounds=RealBounds(0, 1, ""))
prop = Property("prop", value=NominalReal(1.0, ""), template=template)
MeasurementRun("check", material=output, properties=prop)
types = []
recursive_foreach(output, lambda x: types.append(x.typ))
expected = [
"ingredient_run", "material_run", "material_run", "process_run",
"measurement_run", "property_template"
]
assert sorted(types) == sorted(expected)
def test_link_by_uid():
"""Test that linking works."""
root = MaterialRun(name='root', process=ProcessRun(name='root proc'))
leaf = MaterialRun(name='leaf', process=ProcessRun(name='leaf proc'))
IngredientRun(process=root.process, material=leaf)
IngredientRun(process=root.process,
material=LinkByUID.from_entity(leaf, scope='id'))
# Paranoid assertions about equality's symmetry since it's implemented in 2 places
assert root.process.ingredients[0].material == root.process.ingredients[
1].material
assert root.process.ingredients[0].material.__eq__(
root.process.ingredients[1].material)
assert root.process.ingredients[1].material.__eq__(
root.process.ingredients[0].material)
# Verify hash collision on equal LinkByUIDs
assert LinkByUID.from_entity(leaf) in {LinkByUID.from_entity(leaf)}
copy = loads(dumps(root))
assert copy.process.ingredients[0].material == copy.process.ingredients[
1].material
def test_process_run():
"""Test that a process run can house a material, and that it survives serde."""
process_run = ProcessRun("Bake a cake", uids={'My_ID': str(17)})
material_run = MaterialRun("A cake", process=process_run)
# Check that a bi-directional link is established
assert material_run.process == process_run
assert process_run.output_material == material_run
copy_material = loads(dumps(material_run))
assert dumps(copy_material) == dumps(material_run)
assert 'output_material' in repr(process_run)
assert 'process' in repr(material_run)
def test_ingredient_run():
"""Tests that a process can house an ingredient, and that pairing survives serialization."""
# Create a ProcessSpec
proc_run = ProcessRun(name="a process spec", tags=["tag1", "tag2"])
ingred_run = IngredientRun(material=MaterialRun(name='Raw'),
process=proc_run)
# Make copies of both specs
proc_run_copy = loads(dumps(proc_run))
assert proc_run_copy == proc_run, "Full structure wasn't preserved across serialization"
assert 'process' in repr(ingred_run)
assert 'ingredients' in repr(proc_run)
def test_many_ingredients():
"""Test that ingredients remain connected to processes when round-robined through json."""
proc = ProcessRun("foo", spec=ProcessSpec("sfoo"))
expected = []
for i in range(10):
mat = MaterialRun(name=str(i), spec=MaterialSpec("s{}".format(i)))
i_spec = IngredientSpec(name="i{}".format(i), material=mat.spec, process=proc.spec)
IngredientRun(process=proc, material=mat, spec=i_spec)
expected.append("i{}".format(i))
reloaded = loads(dumps(proc))
assert len(list(reloaded.ingredients)) == 10
names = [x.name for x in reloaded.ingredients]
assert sorted(names) == sorted(expected)
def test_equality():
"""Test that equality check works as expected."""
spec = MaterialSpec("A spec",
properties=PropertyAndConditions(
property=Property("a property", value=NominalReal(3, ''))),
tags=["a tag"])
mat1 = MaterialRun("A material", spec=spec)
mat2 = MaterialRun("A material", spec=spec, tags=["A tag"])
assert mat1 == deepcopy(mat1)
assert mat1 != mat2
assert mat1 != "A material"
mat3 = deepcopy(mat1)
assert mat1 == mat3, "Copy somehow failed"
MeasurementRun("A measurement", material=mat3)
assert mat1 != mat3
mat4 = deepcopy(mat3)
assert mat4 == mat3, "Copy somehow failed"
mat4.measurements[0].tags.append('A tag')
assert mat4 != mat3
mat5 = next(x for x in flatten(mat4, 'test-scope') if isinstance(x, MaterialRun))
assert mat5 == mat4, "Flattening removes measurement references, but that's okay"
def test_dictionary_substitution():
"""substitute_objects() should substitute LinkByUIDs that occur in dict keys and values."""
proc = ProcessRun("A process", uids={'id': '123'})
mat = MaterialRun("A material", uids={'generic id': '38f8jf'})
proc_link = LinkByUID.from_entity(proc)
mat_link = LinkByUID.from_entity(mat)
index = {(mat_link.scope.lower(), mat_link.id): mat,
(proc_link.scope.lower(), proc_link.id): proc}
test_dict = {LinkByUID.from_entity(proc): LinkByUID.from_entity(mat)}
subbed = substitute_objects(test_dict, index)
k, v = next((k, v) for k, v in subbed.items())
assert k == proc
assert v == mat
def test_more_iterable_types():
"""Verify recursive_foreach behaves for additional iterable types."""
obj = MaterialRun("foo", tags=["1", "2", "3"])
assert "1" in obj.tags
recursive_foreach({obj}, lambda x: x.tags.remove("1"))
assert "1" not in obj.tags
dct = {obj: obj}
assert "2" in obj.tags
recursive_foreach(dct.keys(), lambda x: x.tags.remove("2"))
assert "2" not in obj.tags
assert "3" in obj.tags
recursive_foreach(dct.values(), lambda x: x.tags.remove("3"))
assert "3" not in obj.tags
def test_scope_substitution():
"""Test that the native id gets serialized, when specified."""
native_id = 'id1'
# Create measurement and material with two ids
mat = MaterialRun("A material", uids={
native_id: str(uuid4()), "an_id": str(uuid4()), "another_id": str(uuid4())})
meas = MeasurementRun("A measurement", material=mat, uids={
"some_id": str(uuid4()), native_id: str(uuid4()), "an_id": str(uuid4())})
# Turn the material pointer into a LinkByUID using native_id
subbed = substitute_links(meas, scope=native_id)
assert subbed.material == LinkByUID.from_entity(mat, scope=native_id)
# Put the measurement into a list and convert that into a LinkByUID using native_id
measurements_list = [meas]
subbed = substitute_links(measurements_list, scope=native_id)
assert subbed == [LinkByUID.from_entity(meas, scope=native_id)]
def test_table():
"""Convert a dictionary to a pandas dataframe and then to a table."""
material = MaterialRun("name")
df = pd.DataFrame.from_records(data)
result = ingest_table(material, df)
assert isinstance(result, MaterialRun)
assert len(result.measurements) == len(data)
filename = "/tmp/table_example.json"
# write to a file (for human inspection)
with open(filename, "w") as f:
dump(result, f, indent=2)
# read it back
with open(filename, "r") as f:
copy = load(f)
assert isinstance(copy, MaterialRun)
def test_thin_dumps():
"""Test that thin_dumps turns pointers into links."""
mat = MaterialRun("The actual material")
meas_spec = MeasurementSpec("measurement", uids={'my_scope': '324324'})
meas = MeasurementRun("The measurement", spec=meas_spec, material=mat)
thin_copy = MeasurementRun.build(json.loads(GEMDJson().thin_dumps(meas)))
assert isinstance(thin_copy, MeasurementRun)
assert isinstance(thin_copy.material, LinkByUID)
assert isinstance(thin_copy.spec, LinkByUID)
assert thin_copy.spec.id == meas_spec.uids['my_scope']
# Check that LinkByUID objects are correctly converted their JSON equivalent
expected_json = '{"id": "my_id", "scope": "scope", "type": "link_by_uid"}'
assert GEMDJson().thin_dumps(LinkByUID('scope', 'my_id')) == expected_json
# Check that objects lacking .uid attributes will raise an exception when dumped
with pytest.raises(TypeError):
GEMDJson().thin_dumps({{'key': 'value'}})