FIX: Corrected the opening process on the chained collections in data…

…base.xsh to put collections into their respective maps rather than the outputs of the iter method.

regolith/database.xsh

@@ -145,29 +145,29 @@ def dump_database(db, client, rc):
         raise ValueError('Do not know how to dump this kind of database')
 
 
-def open_dbs(rc, dbs=None):
+def open_dbs(rc, colls=None):
     """Open the databases
 
     Parameters
     ----------
     rc : RunControl instance
         The rc which has links to the dbs
-    dbs: set or None, optional
+    colls: set or None, optional
         The databases to load. If None load all, defaults to None
 
     Returns
     -------
     client : {FileSystemClient, MongoClient}
         The database client
     """
-    if dbs is None:
-        dbs = []
+    if colls is None:
+        colls = []
     client = ClientManager(rc.databases, rc)
     client.open()
     chained_db = {}
     for db in rc.databases:
-        # if we only want to access some dbs and this db is not in that some
-        db['whitelist'] = dbs
+        # if we only want to access some colls and this db is not in that some
+        db['whitelist'] = colls
         if 'blacklist' not in db:
             db['blacklist'] = ['.travis.yml', '.travis.yaml']
         load_database(db, client, rc)
@@ -176,10 +176,10 @@ def open_dbs(rc, dbs=None):
                 if base not in chained_db:
                     chained_db[base] = ChainCollection()
                 for k, v in coll.items():
-                    if k in chained_db[base]:
-                        chained_db[base][k].maps.append(v)
+                    if k in chained_db[base].fs_map:
+                        chained_db[base].fs_map[k].maps.append(v)
                     else:
-                        chained_db[base][k] = ChainDocument(v)
+                        chained_db[base].fs_map[k] = ChainDocument(v)
             else:
                 if base not in chained_db:
                     chained_db[base] = ChainCollection(coll)
@@ -189,10 +189,10 @@ def open_dbs(rc, dbs=None):
     return client
 
 @contextmanager
-def connect(rc, dbs=None):
+def connect(rc, colls=None):
     """Context manager for ensuring that database is properly setup and torn
     down"""
-    client = open_dbs(rc, dbs=dbs)
+    client = open_dbs(rc, colls=colls)
     yield client
     for db in rc.databases:
         dump_database(db, client, rc)

regolith/main.py

@@ -342,12 +342,12 @@ def main(args=None):
     if rc.cmd in DISCONNECTED_COMMANDS:
         DISCONNECTED_COMMANDS[rc.cmd](rc)
     else:
-        dbs = None
+        colls = None
         if rc.cmd == 'build':
-            dbs = commands.build_db_check(rc)
+            colls = commands.build_db_check(rc)
         elif rc.cmd == 'helper':
-            dbs = commands.helper_db_check(rc)
-        with connect(rc, dbs=dbs) as rc.client:
+            colls = commands.helper_db_check(rc)
+        with connect(rc, colls=colls) as rc.client:
             CONNECTED_COMMANDS[rc.cmd](rc)