def process_item(self, item):
# Define quantities corresponding to materials doc fields
# Attach quantities to materials
item = MontyDecoder().process_decoded(item)
logger.info("Populating material for %s", item['task_id'])
material = Material()
for mkey, property_name in self.materials_symbol_map.items():
value = get(item, mkey)
if value:
material.add_quantity(Quantity(property_name, value))
# Add custom things, e. g. computed entry
computed_entry = get_entry(item)
material.add_quantity(Quantity("computed_entry", computed_entry))
material.add_quantity(
Quantity("external_identifier_mp", item['task_id']))
input_quantities = material.get_quantities()
# Use graph to generate expanded quantity pool
logger.info("Evaluating graph for %s", item['task_id'])
graph = Graph()
graph.remove_models({
"dimensionality_cheon":
DEFAULT_MODEL_DICT['dimensionality_cheon'],
"dimensionality_gorai":
DEFAULT_MODEL_DICT['dimensionality_gorai']
})
new_material = graph.evaluate(material)
# Format document and return
logger.info("Creating doc for %s", item['task_id'])
doc = {"inputs": [quantity.as_dict() for quantity in input_quantities]}
for symbol, quantity in new_material.get_aggregated_quantities().items(
):
all_qs = new_material._symbol_to_quantity[symbol]
# Only add new quantities
if len(all_qs) == 1 and list(all_qs)[0] in input_quantities:
continue
qs = [quantity.as_dict() for quantity in all_qs]
sub_doc = {
"quantities": qs,
"mean": unumpy.nominal_values(quantity.value).tolist(),
"std_dev": unumpy.std_devs(quantity.value).tolist(),
"units": qs[0]['units'],
"title": quantity._symbol_type.display_names[0]
}
doc[symbol.name] = sub_doc
doc.update({
"task_id": item["task_id"],
"pretty_formula": item["pretty_formula"]
})
return jsanitize(doc, strict=True)
class MaterialTest(unittest.TestCase):
def setUp(self):
# Create some test properties and a few base objects
self.q1 = Quantity(
DEFAULT_SYMBOLS['bulk_modulus'],
ureg.Quantity.from_tuple([200, [['gigapascals', 1]]]))
self.q2 = Quantity(
DEFAULT_SYMBOLS['shear_modulus'],
ureg.Quantity.from_tuple([100, [['gigapascals', 1]]]))
self.q3 = Quantity(
DEFAULT_SYMBOLS['bulk_modulus'],
ureg.Quantity.from_tuple([300, [['gigapascals', 1]]]))
self.material = Material()
self.graph = Graph()
def test_material_setup(self):
self.assertTrue(
len(self.material._symbol_to_quantity) == 0,
"Material not initialized properly.")
def test_material_add_quantity(self):
self.material.add_quantity(self.q1)
self.assertEqual(len(self.material._symbol_to_quantity), 1,
"Material did not add the quantity.")
self.material.add_quantity(self.q2)
self.assertEqual(len(self.material._symbol_to_quantity), 2,
"Material did not add quantity to itself.")
def test_material_remove_quantity(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.remove_quantity(self.q1)
self.assertEqual(
len(self.material._symbol_to_quantity[
DEFAULT_SYMBOLS['shear_modulus']]), 1,
"Material did not remove the correct quantity.")
self.material.remove_quantity(self.q2)
self.assertEqual(
len(self.material._symbol_to_quantity[
DEFAULT_SYMBOLS['shear_modulus']]), 0,
"Material did not remove the quantity correctly.")
def test_material_remove_symbol(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.add_quantity(self.q3)
self.material.remove_symbol(DEFAULT_SYMBOLS['bulk_modulus'])
self.assertTrue(
DEFAULT_SYMBOLS['shear_modulus']
in self.material._symbol_to_quantity.keys(),
"Material did not remove Symbol correctly.")
self.assertTrue(
self.q2 in self.material._symbol_to_quantity[
DEFAULT_SYMBOLS['shear_modulus']],
"Material did not remove Symbol correctly.")
self.assertEqual(len(self.material._symbol_to_quantity), 1,
"Material did not remove Symbol correctly.")
def test_get_symbols(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.add_quantity(self.q3)
out = self.material.get_symbols()
self.assertEqual(len(out), 2,
"Material did not get Symbol Types correctly.")
self.assertTrue(DEFAULT_SYMBOLS['bulk_modulus'] in out,
"Material did not get Symbol Types correctly.")
self.assertTrue(DEFAULT_SYMBOLS['shear_modulus'] in out,
"Material did not get Symbol Types correctly.")
def test_get_quantities(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.add_quantity(self.q3)
out = self.material.get_quantities()
self.assertTrue(all([q in out for q in [self.q1, self.q2, self.q3]]),
"Material did not get Quantity objects correctly.")
def test_get_aggregated_quantities(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.add_quantity(self.q3)
agg = self.material.get_aggregated_quantities()
def process_item(self, item):
# Define quantities corresponding to materials doc fields
# Attach quantities to materials
item = MontyDecoder().process_decoded(item)
logger.info("Populating material for %s", item['task_id'])
material = Material()
if 'created_at' in item.keys():
date_created = item['created_at']
else:
date_created = ""
provenance = ProvenanceElement(
source={
"source": self.source_name,
"source_key": item['task_id'],
"date_created": date_created
})
for mkey, property_name in self.materials_symbol_map.items():
value = get(item, mkey)
if value:
material.add_quantity(
QuantityFactory.create_quantity(property_name,
value,
provenance=provenance))
# Add custom things, e. g. computed entry
computed_entry = get_entry(item)
material.add_quantity(
QuantityFactory.create_quantity("computed_entry",
computed_entry,
provenance=provenance))
material.add_quantity(
QuantityFactory.create_quantity("external_identifier_mp",
item['task_id'],
provenance=provenance))
input_quantities = material.get_quantities()
# Use graph to generate expanded quantity pool
logger.info("Evaluating graph for %s", item['task_id'])
graph = Graph()
graph.remove_models({
"dimensionality_cheon":
DEFAULT_MODEL_DICT['dimensionality_cheon'],
"dimensionality_gorai":
DEFAULT_MODEL_DICT['dimensionality_gorai']
})
new_material = graph.evaluate(material)
# Format document and return
logger.info("Creating doc for %s", item['task_id'])
# Gives the initial inputs that were used to derive properties of a
# certain material.
doc = {
"inputs":
[StorageQuantity.from_quantity(q) for q in input_quantities]
}
for symbol, quantity in new_material.get_aggregated_quantities().items(
):
all_qs = new_material._symbol_to_quantity[symbol]
# Only add new quantities
# TODO: Condition insufficiently general.
# Can end up with initial quantities added as "new quantities"
if len(all_qs) == 1 and list(all_qs)[0] in input_quantities:
continue
# Write out all quantities as dicts including the
# internal ID for provenance tracing
qs = [StorageQuantity.from_quantity(q).as_dict() for q in all_qs]
# THE listing of all Quantities of a given symbol.
sub_doc = {
"quantities": qs,
"mean": unumpy.nominal_values(quantity.value).tolist(),
"std_dev": unumpy.std_devs(quantity.value).tolist(),
"units":
quantity.units.format_babel() if quantity.units else None,
"title": quantity._symbol_type.display_names[0]
}
# Symbol Name -> Sub_Document, listing all Quantities of that type.
doc[symbol.name] = sub_doc
doc.update({
"task_id": item["task_id"],
"pretty_formula": item["pretty_formula"]
})
return jsanitize(doc, strict=True)
class MaterialTest(unittest.TestCase):
def setUp(self):
# Create some test properties and a few base objects
self.q1 = QuantityFactory.create_quantity(DEFAULT_SYMBOLS['bulk_modulus'],
ureg.Quantity.from_tuple([200, [['gigapascals', 1]]]))
self.q2 = QuantityFactory.create_quantity(DEFAULT_SYMBOLS['shear_modulus'],
ureg.Quantity.from_tuple([100, [['gigapascals', 1]]]))
self.q3 = QuantityFactory.create_quantity(DEFAULT_SYMBOLS['bulk_modulus'],
ureg.Quantity.from_tuple([300, [['gigapascals', 1]]]))
self.material = Material()
self.graph = Graph()
def test_material_setup(self):
self.assertTrue(len(self.material._symbol_to_quantity) == 0,
"Material not initialized properly.")
def test_material_add_quantity(self):
self.material.add_quantity(self.q1)
self.assertEqual(len(self.material._symbol_to_quantity), 1,
"Material did not add the quantity.")
self.material.add_quantity(self.q2)
self.assertEqual(len(self.material._symbol_to_quantity), 2,
"Material did not add quantity to itself.")
def test_material_remove_quantity(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.remove_quantity(self.q1)
self.assertEqual(
len(self.material._symbol_to_quantity[DEFAULT_SYMBOLS['shear_modulus']]),
1, "Material did not remove the correct quantity.")
self.material.remove_quantity(self.q2)
self.assertEqual(
len(self.material._symbol_to_quantity[DEFAULT_SYMBOLS['shear_modulus']]),
0, "Material did not remove the quantity correctly.")
def test_material_remove_symbol(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.add_quantity(self.q3)
self.material.remove_symbol(DEFAULT_SYMBOLS['bulk_modulus'])
self.assertTrue(
DEFAULT_SYMBOLS['shear_modulus'] in self.material._symbol_to_quantity.keys(),
"Material did not remove Symbol correctly.")
self.assertTrue(
self.q2 in self.material._symbol_to_quantity[DEFAULT_SYMBOLS['shear_modulus']],
"Material did not remove Symbol correctly.")
self.assertEqual(len(self.material._symbol_to_quantity), 1,
"Material did not remove Symbol correctly.")
def test_get_symbols(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.add_quantity(self.q3)
out = self.material.get_symbols()
self.assertEqual(
len(out), 2, "Material did not get Symbol Types correctly.")
self.assertTrue(DEFAULT_SYMBOLS['bulk_modulus'] in out,
"Material did not get Symbol Types correctly.")
self.assertTrue(DEFAULT_SYMBOLS['shear_modulus'] in out,
"Material did not get Symbol Types correctly.")
def test_get_quantities(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.add_quantity(self.q3)
out = self.material.get_quantities()
self.assertTrue(all([q in out for q in [self.q1, self.q2, self.q3]]),
"Material did not get Quantity objects correctly.")
def test_get_aggregated_quantities(self):
self.material.add_quantity(self.q1)
self.material.add_quantity(self.q2)
self.material.add_quantity(self.q3)
agg = self.material.get_aggregated_quantities()
# TODO: add a meaningful test here
def test_add_default_quantities(self):
material = Material(add_default_quantities=True)
self.assertEqual(list(material['temperature'])[0],
QuantityFactory.create_quantity("temperature", 300,
provenance=ProvenanceElement(model='default')))
self.assertEqual(list(material['relative_permeability'])[0],
QuantityFactory.create_quantity("relative_permeability", 1,
provenance=ProvenanceElement(model='default')))