changes to database connection code to support "authsource" parameter in db file

Author: computron

atomate/feff/database.py

@@ -19,8 +19,9 @@
 class FeffCalcDb(CalcDb):
 
     def __init__(self, host="localhost", port=27017, database="feff", collection="tasks", user=None,
-                 password=None):
-        super(FeffCalcDb, self).__init__(host, port, database, collection, user, password)
+                 password=None, **kwargs):
+        super(FeffCalcDb, self).__init__(host, port, database, collection,
+                                         user, password, **kwargs)
 
     def build_indexes(self, indexes=None, background=True):
         _indexes = indexes if indexes else ["structure.formula"]

atomate/lammps/database.py

@@ -21,8 +21,9 @@
 class LammpsCalcDb(CalcDb):
 
     def __init__(self, host="localhost", port=27017, database="lammps", collection="tasks",
-                 user=None, password=None):
-        super(LammpsCalcDb, self).__init__(host, port, database, collection, user, password)
+                 user=None, password=None, **kwargs):
+        super(LammpsCalcDb, self).__init__(host, port, database, collection,
+                                           user, password, **kwargs)
 
     def build_indexes(self, indexes=None, background=True):
         indexes = indexes or []

atomate/qchem/database.py

@@ -25,9 +25,10 @@ def __init__(self,
                  database="qchem",
                  collection="tasks",
                  user=None,
-                 password=None):
+                 password=None,
+                 **kwargs):
         super(QChemCalcDb, self).__init__(host, port, database, collection,
-                                          user, password)
+                                          user, password, **kwargs)
 
     def build_indexes(self, indexes=None, background=True):
         """

atomate/utils/database.py

@@ -25,14 +25,17 @@
 
 class CalcDb(six.with_metaclass(ABCMeta)):
 
-    def __init__(self, host, port, database, collection, user, password):
+    def __init__(self, host, port, database, collection, user, password, **kwargs):
         self.host = host
         self.db_name = database
         self.user = user
         self.password = password
         self.port = int(port)
+
         try:
-            self.connection = MongoClient(self.host, self.port)
+            self.connection = MongoClient(host=self.host, port=self.port,
+                                          username=self.user,
+                                          password=self.password, **kwargs)
             self.db = self.connection[self.db_name]
         except:
             logger.error("Mongodb connection failed")
@@ -122,5 +125,9 @@ def from_db_file(cls, db_file, admin=True):
             user = creds.get("readonly_user")
             password = creds.get("readonly_password")
 
+        kwargs = {}
+        if "authsource" in creds:
+            kwargs["authsource"] = creds["authsource"]
+
         return cls(creds["host"], int(creds["port"]), creds["database"], creds["collection"],
-                   user, password)
+                   user, password, **kwargs)

atomate/utils/utils.py

@@ -337,15 +337,23 @@ def get_uri(dir_name):
 
 def get_database(config_file=None, settings=None, admin=False, **kwargs):
     d = loadfn(config_file) if settings is None else settings
-    conn = MongoClient(host=d["host"], port=d["port"], **kwargs)
-    db = conn[d["database"]]
+
     try:
         user = d["admin_user"] if admin else d["readonly_user"]
         passwd = d["admin_password"] if admin else d["readonly_password"]
-        db.authenticate(user, passwd)
     except (KeyError, TypeError, ValueError):
         logger.warning("No {admin,readonly}_user/password found in config. file, "
             "accessing DB without authentication")
+        user = None
+        passwd = None
+
+    if "authsource" in d and "authsource" not in kwargs:
+        kwargs["authsource"] = d["authsource"]
+
+    conn = MongoClient(host=d["host"], port=d["port"], username=user,
+                       password=passwd, **kwargs)
+    db = conn[d["database"]]
+
     return db
 
 

atomate/vasp/database.py

@@ -34,8 +34,9 @@ class VaspCalcDb(CalcDb):
     """
 
     def __init__(self, host="localhost", port=27017, database="vasp", collection="tasks", user=None,
-                 password=None):
-        super(VaspCalcDb, self).__init__(host, port, database, collection, user, password)
+                 password=None, **kwargs):
+        super(VaspCalcDb, self).__init__(host, port, database, collection, user,
+                                         password, **kwargs)
 
     def build_indexes(self, indexes=None, background=True):
         """