def process(self, item):
if self.graph_parallel and not self.allow_child_process and \
current_process().name != "MainProcess":
logger.warning(
"It appears derive_quantities() is running "
"in a child process, possibly in a parallelized "
"Runner.\nThis is not recommended and will deteriorate "
"performance.")
# 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 = None
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 = pydash.get(item, mkey)
if value:
material.add_quantity(
QuantityFactory.create_quantity(
property_name,
value,
units=Registry("units").get(property_name, None),
provenance=provenance))
# Add custom things, e. g. computed entry
computed_entry = get_entry(item)
if computed_entry:
material.add_quantity(
QuantityFactory.create_quantity("computed_entry",
computed_entry,
provenance=provenance))
else:
logger.info("Unable to create computed entry for {}".format(
item['task_id']))
material.add_quantity(
QuantityFactory.create_quantity("external_identifier_mp",
item['task_id'],
provenance=provenance))
input_quantities = material.symbol_quantities_dict
# Use graph to generate expanded quantity pool
logger.info("Evaluating graph for %s", item['task_id'])
new_material = self._graph_evaluator.evaluate(
material, timeout=self.graph_timeout)
# 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 chain.from_iterable(input_quantities.values())
]
}
for symbol, quantities in new_material.symbol_quantities_dict.items():
# If no new quantities of a given symbol were derived (i.e. if the initial
# input quantity/ies is/are the only one/s listed in the new material) then don't add
# that quantity to the propnet entry document as a derived quantity.
if len(quantities) == len(input_quantities[symbol]):
continue
sub_doc = {}
try:
# Write out all quantities as dicts including the
# internal ID for provenance tracing
qs = [
jsanitize(StorageQuantity.from_quantity(q), strict=True)
for q in quantities
]
except AttributeError as ex:
# Check to see if this is an error caused by an object
# that is not JSON serializable
msg = ex.args[0]
if "object has no attribute 'as_dict'" in msg:
# Write error to db and logger
errmsg = "Quantity of Symbol '{}' is not ".format(symbol.name) + \
"JSON serializable. Cannot write quantities to database!"
logger.error(errmsg)
sub_doc['error'] = errmsg
qs = []
else:
# If not, re-raise the error
raise ex
sub_doc['quantities'] = qs
doc[symbol.name] = sub_doc
aggregated_quantities = new_material.get_aggregated_quantities()
for symbol, quantity in aggregated_quantities.items():
if symbol.name not in doc:
# No new quantities were derived
continue
# Store mean and std dev for aggregated quantities
sub_doc = {
"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.display_names[0]
}
# Symbol Name -> Sub_Document, listing all Quantities of that type.
doc[symbol.name].update(sub_doc)
doc.update({
"task_id": item["task_id"],
"pretty_formula": item.get("pretty_formula"),
"deprecated": item.get("deprecated", False)
})
if self.include_sandboxed:
doc.update({'sbxn': item.get("sbxn", [])})
return jsanitize(doc, strict=True)
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)
