def test_init_file(self):
"""Create DBConfig from file or path.
"""
# sending file obj, or its path, should have same effect
d1 = DBConfig(config_file=self.tmp)
d2 = DBConfig(config_file=self.tmp.name)
self.assertEqual(d1.settings, d2.settings)
self.assertEqual(d2.settings, self._aliased_cfg())
def test_init_file(self):
"""Create DBConfig from file or path.
"""
# sending file obj, or its path, should have same effect
tmp = "dbconfigtest.json"
with open(tmp, "w") as f:
json.dump(self.cfg, f)
f.flush()
# reset file to beginning
with open(tmp, "r") as f:
d1 = DBConfig(config_file=f)
d2 = DBConfig(config_file=tmp)
self.assertEqual(d1.settings, d2.settings)
self.assertEqual(d2.settings, self._aliased_cfg())
def __init__(self, config_dict=None):
"""
enabled: no
database: abinit
collection: test
#host: 0.0.0.0
#port: 8080
#user: gmatteo
#password: helloworld
"""
self.config = {}
# Don't initialize DBConfig if not dict or dict contains `enabled: no`
if config_dict and config_dict.pop("enabled", True):
self.config = DBConfig(config_dict=config_dict)
def store_reaxys_reactions_db(reactions,
dbfile="db.json",
collection="reactions"):
"""
Insert reaction information into a MongoDB database.
:param reactions: List of reactions, defined as above.
:param dbfile: A config file indicating the database into which the
reactions will be inserted.
:param collection: Collection within the database in which to store
the reactions.
:return: List of rxn_ids that were
"""
# Set up MongoDB database with pymatgen-db and pymongo
config = DBConfig(config_file=dbfile)
client = MongoClient(config.host,
config.port,
username=config.user,
password=config.password)
db = client[config.dbname]
collection = db[collection]
just_added = []
if "rxn_id" not in collection.index_information():
collection.create_index("rxn_id", unique=True)
for reaction in reactions:
try:
reaction["rxn_id"] = reaction["meta"]["rxn_id"]
collection.insert_one(reaction)
just_added.append(reaction["rxn_id"])
except:
continue
return just_added
def test_init_dict(self):
"""Create DBConfig from dict object.
"""
d1 = DBConfig(config_dict=self.cfg)
self.assertEqual(d1.settings, self._aliased_cfg())
def get_settings(config_file):
cfg = DBConfig(config_file)
return cfg.settings