def update_targets(self, items: List[List[Dict]]):
"""
Inserts the new task_types into the task_types collection
Args:
items ([([dict],[int])]): A list of tuples of materials to update and the corresponding
processed task_ids
"""
items = list(filter(None, chain.from_iterable(items)))
for item in items:
item.update({"_bt": self.timestamp})
material_ids = list({item["material_id"] for item in items})
if len(items) > 0:
self.logger.info(f"Updating {len(items)} materials")
self.materials.remove_docs({self.materials.key: {"$in": material_ids}})
self.materials.update(
docs=jsanitize(items, allow_bson=True),
key=["material_id"],
)
else:
self.logger.info("No items to update")
def update_targets(self, items):
"""
Inserts the thermo docs into the thermo collection
Args:
items ([[dict]]): a list of list of thermo dictionaries to update
"""
# flatten out lists
items = list(filter(None, chain.from_iterable(items)))
# Check if already updated this run
items = [
i for i in items if i[self.thermo.key] not in self._completed_tasks
]
self._completed_tasks |= {i[self.thermo.key] for i in items}
for item in items:
if isinstance(item["last_updated"], dict):
item["last_updated"] = MontyDecoder().process_decoded(
item["last_updated"])
if len(items) > 0:
self.logger.info(f"Updating {len(items)} thermo documents")
self.thermo.update(docs=jsanitize(items), key=[self.thermo.key])
else:
self.logger.info("No items to update")
def process_item(self, item) -> Dict:
"""
- Add volume information to each entry to create the insertion electrode document
- Add the host structure
"""
if item is None:
return None
self.logger.debug(
f"Working on {item['group_id']} with {len(item['thermo_docs'])}")
entries = [
tdoc_["entries"][tdoc_["energy_type"]]
for tdoc_ in item["thermo_docs"]
]
entries = list(map(ComputedStructureEntry.from_dict, entries))
working_ion_entry = ComputedEntry.from_dict(
item["working_ion_doc"]["entries"][item["working_ion_doc"]
["energy_type"]])
working_ion = working_ion_entry.composition.reduced_formula
decomp_energies = {
d_["material_id"]: d_["energy_above_hull"]
for d_ in item["thermo_docs"]
}
least_wion_ent = min(
entries,
key=lambda x: x.composition.get_atomic_fraction(working_ion))
host_structure = least_wion_ent.structure.copy()
host_structure.remove_species([item["working_ion"]])
for ient in entries:
ient.data["volume"] = ient.structure.volume
ient.data["decomposition_energy"] = decomp_energies[ient.entry_id]
ie = InsertionElectrodeDoc.from_entries(
grouped_entries=entries,
working_ion_entry=working_ion_entry,
battery_id=item["group_id"],
host_structure=host_structure,
)
if ie is None:
return None # {"failed_reason": "unable to create InsertionElectrode document"}
return jsanitize(ie.dict())
def test_jsanitize():
"""
Tests emmet Jsanitize which converts MSONable classes into dicts
"""
# clean_json should have no effect on None types.
d = {"hello": 1, "world": None}
clean = jsanitize(d)
assert clean["world"] is None
assert json.loads(json.dumps(d)) == json.loads(json.dumps(clean))
d = {"hello": GoodMSONClass(1, 2, 3)}
with pytest.raises(TypeError):
json.dumps(d)
clean = jsanitize(d)
assert isinstance(clean["hello"], dict)
clean_strict = jsanitize(d, strict=True)
assert clean_strict["hello"]["a"] == 1
assert clean_strict["hello"]["b"] == 2
d = {"dt": datetime.datetime.now()}
clean = jsanitize(d)
assert isinstance(clean["dt"], str)
clean = jsanitize(d, allow_bson=True)
assert isinstance(clean["dt"], datetime.datetime)
d = {
"a": ["b", np.array([1, 2, 3])],
"b": ObjectId.from_datetime(datetime.datetime.now()),
}
clean = jsanitize(d)
assert clean["a"] == ["b", [1, 2, 3]]
assert isinstance(clean["b"], str)
rnd_bin = bytes(np.random.rand(10))
d = {"a": bytes(rnd_bin)}
clean = jsanitize(d, allow_bson=True)
assert clean["a"] == bytes(rnd_bin)
assert isinstance(clean["a"], bytes)
def _post_resource(
self,
body: Dict = None,
params: Optional[Dict] = None,
monty_decode: bool = True,
suburl: Optional[str] = None,
use_document_model: Optional[bool] = True,
):
"""
Post data to the endpoint for a Resource.
Arguments:
body: body json to send in post request
params: extra params to send in post request
monty_decode: Decode the data using monty into python objects
suburl: make a request to a specified sub-url
use_document_model: whether to use the core document model for data reconstruction
Returns:
A Resource, a dict with two keys, "data" containing a list of documents, and
"meta" containing meta information, e.g. total number of documents
available.
"""
check_limit()
payload = jsanitize(body)
try:
url = self.endpoint
if suburl:
url = urljoin(self.endpoint, suburl)
if not url.endswith("/"):
url += "/"
response = self.session.post(url,
json=payload,
verify=True,
params=params)
if response.status_code == 200:
if monty_decode:
data = json.loads(response.text, cls=MontyDecoder)
else:
data = json.loads(response.text)
if self.document_model and use_document_model:
data["data"] = [
self.document_model.parse_obj(d) for d in data["data"]
] # type: ignore
return data
else:
try:
data = json.loads(response.text)["detail"]
except (JSONDecodeError, KeyError):
data = "Response {}".format(response.text)
if isinstance(data, str):
message = data
else:
try:
message = ", ".join(
"{} - {}".format(entry["loc"][1], entry["msg"])
for entry in data)
except (KeyError, IndexError):
message = str(data)
raise MPRestError(
f"REST post query returned with error status code {response.status_code} "
f"on URL {response.url} with message:\n{message}")
except RequestException as ex:
raise MPRestError(str(ex))