def connect(self, force_reset=False):
if not self._collection or force_reset:
if self.mgclient_config_path:
config = Config(check=check, path=self.mgclient_config_path)
client = Client(config)
else:
client = Client()
db = client.db(self.mongogrant_spec)
self._collection = db[self.collection_name]
class MDB:
cmp_tbl = {
">": "$gt",
">=": "$gte",
"<": "$lt",
"<=": "$lte",
"==": "$eq",
"!=": "$ne"
}
def __init__(self):
from mongogrant import Client
self.client = Client()
self.core_db = self.client.db("ro:dev/optimade_core")
def get_structure(self, structure_id):
doc = self.core_db.materials.find_one({"task_id": structure_id})
if doc:
return Structure.from_material_doc(doc)
def get_structures(self, filter_):
match = re.search(r'nelements([^0-9]+)([0-9]+)', filter_)
if match:
comp, n = match.groups()
crit = {"nelements": {self.cmp_tbl[comp]: int(n)}}
return [
Structure.from_material_doc(doc)
for doc in mdb.core_db.materials.find(
crit, Structure.material_doc_projection())
]
else:
return []
def __init__(
self,
mongogrant_spec: str,
collection_name: str,
mgclient_config_path: Optional[str] = None,
**kwargs,
):
"""
Args:
mongogrant_spec: of the form `<role>`:`<host>`/`<db>`, where
role is one of {"read", "readWrite"} or aliases {"ro", "rw"};
host is a db host (w/ optional port) or alias; and db is a db
on that host, or alias. See mongogrant documentation.
collection_name: name of mongo collection
mgclient_config_path: Path to mongogrant client config file,
or None if default path (`mongogrant.client.path`).
"""
self.mongogrant_spec = mongogrant_spec
self.collection_name = collection_name
self.mgclient_config_path = mgclient_config_path
self._collection = None
if self.mgclient_config_path:
config = Config(check=check, path=self.mgclient_config_path)
client = Client(config)
else:
client = Client()
if set(("username", "password", "database", "host")) & set(kwargs):
raise StoreError("MongograntStore does not accept "
"username, password, database, or host "
"arguments. Use `mongogrant_spec`.")
self.kwargs = kwargs
_auth_info = client.get_db_auth_from_spec(self.mongogrant_spec)
super(MongograntStore, self).__init__(
host=_auth_info["host"],
database=_auth_info["authSource"],
username=_auth_info["username"],
password=_auth_info["password"],
collection_name=self.collection_name,
**kwargs,
)
def mgrant_user(mgrant_server):
config_path, mdport, dbname = mgrant_server
config = Config(check=check, path=config_path, seed=seed())
client = Client(config)
client.set_auth(
host=f"localhost:{mdport}",
db=dbname,
role="read",
username="******",
password="******",
)
client.set_auth(
host=f"localhost:{mdport}",
db=dbname,
role="readWrite",
username="******",
password="******",
)
client.set_alias("testhost", f"localhost:{mdport}", which="host")
client.set_alias("testdb", dbname, which="db")
return client
def setUpClass(cls):
# `nosetests` does not see class decorators
# https://github.com/nose-devs/nose/issues/946
if "TRAVIS" in os.environ and os.environ["TRAVIS"] == "true":
raise unittest.SkipTest("Skipping this test on Travis CI.")
cls.client = Client()
cls.db_stag = cls.client.db("ro:staging/mp_core")
cls.db_prod = cls.client.db("ro:prod/mp_emmet_prod")
cls.db_phonons = cls.client.db("ro:prod/phonondb")
cls.mats_stag = cls.db_stag.materials
cls.mats_prod = cls.db_prod.materials
idset_stag = set(cls.mats_stag.distinct("task_id"))
idset_prod = set(cls.mats_prod.distinct("task_id"))
n_new_ids = len(idset_stag - idset_prod)
if n_new_ids:
logging.info("{} new material ids".format(n_new_ids))
n_retiring_ids = len(idset_prod - idset_stag)
if n_retiring_ids:
logging.warning("{} retiring material ids".format(n_retiring_ids))
@app.route('/cubism')
def cubism():
return current_app.send_static_file('cubism.v1.js')
@app.route('/structureViewer')
def structure_viewer():
return current_app.send_static_file('structureViewerBuilt.js')
@app.route("/container")
def get_style():
return current_app.send_static_file('container.css')
client = Client()
client.set_alias("mg2.lbl", "matgen2.lbl.gov", "host")
client.set_alias("m01.nersc", "mongodb01.nersc.gov", "host")
client.set_alias("m03.nersc", "mongodb03.nersc.gov", "host")
client.set_alias("m04.nersc", "mongodb04.nersc.gov", "host")
client.set_alias("build", "mp_prod", "db")
client.set_alias("core", "fw_mp_prod_atomate", "db")
client.set_alias("app", "mg_apps_prod", "db")
client.set_alias("elastic", "fw_jhm_kpoints", "db")
client.set_alias("SCAN", "fw_shyamd", "db")
dbs = {
"elastic": client.db("ro:m03.nersc/elastic", connect=False),
"SCAN": client.db("ro:m03.nersc/SCAN", connect=False),
from mongogrant import Client
app = Flask(__name__)
@app.route('/')
def hello_world():
return current_app.send_static_file('main.html')
@app.route('/cubism')
def cubism():
return current_app.send_static_file('cubism.v1.js')
client = Client()
client.set_alias("m01.nersc", "mongodb01.nersc.gov", "host")
client.set_alias("m03.nersc", "mongodb03.nersc.gov", "host")
client.set_alias("core", "fw_mp_prod_atomate", "db")
client.set_alias("elastic", "fw_jhm_kpoints", "db")
client.set_alias("SCAN", "fw_shyamd", "db")
dbs = {
"elastic": client.db("ro:m03.nersc/elastic", connect=False),
"SCAN": client.db("ro:m03.nersc/SCAN", connect=False),
"core": client.db("ro:m01.nersc/core", connect=False),
}
def __init__(self):
from mongogrant import Client
self.client = Client()
self.core_db = self.client.db("ro:dev/optimade_core")
import numpy as np
from tqdm import tqdm
from emmet.common.utils import get_chemsys_space
html_out = len(sys.argv) > 1 and sys.argv[1] == 'html'
if html_out:
sys_print = print
def print(s=None):
s = s or ""
sys_print(s + "<br>")
print("Connecting to databases and retrieving on-hull materials...")
client = Client()
db_stag = client.db("ro:staging/mp_core")
db_prod = client.db("ro:production/mp_emmet_prod")
onhull_prod = db_prod.materials.distinct("task_id", {
"e_above_hull": 0,
"deprecated": {
"$ne": True
}
})
onhull_stag = db_stag.materials.distinct("task_id", {
"e_above_hull": 0,
"deprecated": False
})
onhull_prod_but_not_stag = set(onhull_prod) - set(onhull_stag)
print(