def save(self, data):
data = utils.to_list(data)
if len(data) == 0:
return []
group = self._refine_group_from_data(self.GROUP, data)
return Key(self._save(group, data))
def remove_records(self, key):
self.__make_connection()
return self.__collection.delete({
'_id': {
'$in': utils.to_list(key)
}
}).deleted_count
def activate_records(self, key):
self.__make_connection()
return self.__collection.update_many(
{'_id': {
'$in': utils.to_list(key)
}}, {'$set': {
'completed': False
}})
def mark_complete(self, key):
self.__make_connection()
return self.__collection.update_many(
{'_id': {
'$in': utils.to_list(key)
}}, {'$set': {
'completed': True
}})
def remove_dataset(self, datasets):
datasets = utils.to_list(datasets)
with HDF5File() as file:
group = file[self.GROUP]
for dataset in self._get_datasets(group):
if dataset in datasets:
self._remove_index_data(
self.GROUP, Key(list(group[dataset].attrs.keys())))
del group[dataset]
return True
def save(self, data):
self.__make_connection()
try:
return self.__collection.insert_many(utils.to_list(data),
ordered=False).inserted_ids
except BulkWriteError as err:
self.failed_instances.extend([
failed_instance['op']
for failed_instance in err.details['writeErrors']
])
print(
f'Failed to write {len(self.failed_instances)} {self.COLLECTION}s! These are probably duplicates, but dumping to data directory anyway...',
flush=True)
utils.save_json(
json.loads(json_util.dumps(self.failed_instances)),
utils.rotate_file(
os.path.join(config.DATA_DIR, f'{self.COLLECTION}.json')))
self.failed_instances = []
def test_to_list(data, length):
ls_data = utils.to_list(data)
assert isinstance(ls_data, (list, tuple))
assert all(map(lambda x: isinstance(x, dict), ls_data))
assert len(ls_data) == length
def __init__(self, impl=None):
self.impl = impl or rxns.create_intramolecular_reactions()
self.impl = utils.to_list(self.impl)
def __init__(self, impl=None):
self.impl = impl or rxns.create_intermolecular_reactions()
self.impl = utils.to_list(self.impl)
self.backbones = list(
map(lambda x: x.mol,
repo.create_backbone_repository().load()))