Changed DB root-object-initialization to use an open connection and more

This fixes #84.

Also:

- Added missing transaction ``begin`` call in the DB ``transaction()``
  context manager.

- Added the ability to add a transaction note whan calling
  ``transaction()``.  This is useful (as would be the ability to pass
  in other transaction meta data, but this was needed by (and this
  tested) to make an existing test pass.

src/ZODB/Connection.py

@@ -190,7 +190,6 @@ def before_instance(before):
 
         self._reader = ObjectReader(self, self._cache, self._db.classFactory)
 
-
     def add(self, obj):
         """Add a new object 'obj' to the database and assign it an oid."""
         if self.opened is None:
@@ -202,19 +201,22 @@ def add(self, obj):
             raise TypeError("Only first-class persistent objects may be"
                             " added to a Connection.", obj)
         elif obj._p_jar is None:
-            assert obj._p_oid is None
-            oid = obj._p_oid = self.new_oid()
-            obj._p_jar = self
-            if self._added_during_commit is not None:
-                self._added_during_commit.append(obj)
-            self._register(obj)
-            # Add to _added after calling register(), so that _added
-            # can be used as a test for whether the object has been
-            # registered with the transaction.
-            self._added[oid] = obj
+            self._add(obj, self.new_oid())
         elif obj._p_jar is not self:
             raise InvalidObjectReference(obj, obj._p_jar)
 
+    def _add(self, obj, oid):
+        assert obj._p_oid is None
+        oid = obj._p_oid = oid
+        obj._p_jar = self
+        if self._added_during_commit is not None:
+            self._added_during_commit.append(obj)
+        self._register(obj)
+        # Add to _added after calling register(), so that _added
+        # can be used as a test for whether the object has been
+        # registered with the transaction.
+        self._added[oid] = obj
+
     def get(self, oid):
         """Return the persistent object with oid 'oid'."""
         if self.opened is None:

src/ZODB/DB.py

@@ -39,6 +39,7 @@
 from persistent.TimeStamp import TimeStamp
 import six
 
+from . import POSException
 
 logger = logging.getLogger('ZODB.DB')
 
@@ -211,7 +212,8 @@ def availableGC(self):
         """Perform garbage collection on available connections.
 
         If a connection is no longer viable because it has timed out, it is
-        garbage collected."""
+        garbage collected.
+        """
         threshhold = time.time() - self.timeout
 
         to_remove = ()
@@ -442,30 +444,6 @@ def __init__(self, storage,
                 DeprecationWarning, 2)
             storage.tpc_vote = lambda *args: None
 
-        temp_storage = self._mvcc_storage.new_instance()
-        try:
-            try:
-                temp_storage.poll_invalidations()
-                temp_storage.load(z64)
-            except KeyError:
-                # Create the database's root in the storage if it doesn't exist
-                from persistent.mapping import PersistentMapping
-                root = PersistentMapping()
-                # Manually create a pickle for the root to put in the storage.
-                # The pickle must be in the special ZODB format.
-                file = BytesIO()
-                p = Pickler(file, _protocol)
-                p.dump((root.__class__, None))
-                p.dump(root.__getstate__())
-                t = transaction.Transaction()
-                t.description = 'initial database creation'
-                temp_storage.tpc_begin(t)
-                temp_storage.store(z64, None, file.getvalue(), '', t)
-                temp_storage.tpc_vote(t)
-                temp_storage.tpc_finish(t)
-        finally:
-            temp_storage.release()
-
         # Multi-database setup.
         if databases is None:
             databases = {}
@@ -479,6 +457,15 @@ def __init__(self, storage,
 
         self.large_record_size = large_record_size
 
+        # Make sure we have a root:
+        with self.transaction('initial database creation') as conn:
+            try:
+                conn.get(z64)
+            except KeyError:
+                from persistent.mapping import PersistentMapping
+                root = PersistentMapping()
+                conn._add(root, z64)
+
     @property
     def _storage(self):      # Backward compatibility
         return self.storage
@@ -906,8 +893,8 @@ def undo(self, id, txn=None):
         """
         self.undoMultiple([id], txn)
 
-    def transaction(self):
-        return ContextManager(self)
+    def transaction(self, note=None):
+        return ContextManager(self, note)
 
     def new_oid(self):
         return self.storage.new_oid()
@@ -926,12 +913,16 @@ class ContextManager:
     """PEP 343 context manager
     """
 
-    def __init__(self, db):
+    def __init__(self, db, note=None):
         self.db = db
+        self.note = note
 
     def __enter__(self):
-        self.tm = transaction.TransactionManager()
+        self.tm = tm = transaction.TransactionManager()
         self.conn = self.db.open(self.tm)
+        t = tm.begin()
+        if self.note:
+            t.note(self.note)
         return self.conn
 
     def __exit__(self, t, v, tb):

src/ZODB/tests/dbopen.txt

@@ -126,6 +126,7 @@ returned are distinct:
     >>> st = Storage()
     >>> db = DB(st)
     >>> c1 = db.open()
+    >>> c1.cacheMinimize()
     >>> c2 = db.open()
     >>> c3 = db.open()
     >>> c1 is c2 or c1 is c3 or c2 is c3
@@ -260,6 +261,7 @@ closed one out of the available connection stack.
     >>> st = Storage()
     >>> db = DB(st, pool_size=3)
     >>> conns = [db.open() for dummy in range(6)]
+    >>> conns[0].cacheMinimize()
     >>> len(handler.records)  # 3 warnings for the "excess" connections
     3
     >>> pool = db.pool
@@ -328,6 +330,7 @@ resources (like RDB connections), for the duration.
     >>> st = Storage()
     >>> db = DB(st, pool_size=2)
     >>> conn0 = db.open()
+    >>> conn0.cacheMinimize() # See fix84.rst
     >>> len(conn0._cache)  # empty now
     0
     >>> import transaction

src/ZODB/tests/fix84.rst

@@ -0,0 +1,19 @@
+A change in the way databases were initialized affected tests
+=============================================================
+
+Originally, databases added root objects by interacting directly with
+storages, rather than using connections.  As storages transaction
+interaction became more complex, interacting directly with storages
+let to duplicated code (and buggy) code.
+
+See: https://github.com/zopefoundation/ZODB/issues/84
+
+Fixing this had some impacts that affected tests:
+
+- New databases now have a connection with a single object in it's cache.
+  This is a very slightly good thing, but it broke some tests expectations.
+
+- Tests that manipulated time, had their clocks off because of new time calls.
+
+This led to some test fixes, in many cases adding a mysterious
+``cacheMinimize()`` call.

src/ZODB/tests/synchronizers.txt

@@ -21,6 +21,7 @@ Make a change locally:
 
     >>> st = SimpleStorage()
     >>> db = ZODB.DB(st)
+    >>> st.sync_called = False
     >>> cn = db.open()
     >>> rt = cn.root()
     >>> rt['a'] = 1

src/ZODB/tests/testCache.py

@@ -237,8 +237,8 @@ def testLRU(self):
             # not bother to check this
 
     def testSize(self):
+        self.db.cacheMinimize()
         self.assertEqual(self.db.cacheSize(), 0)
-        self.assertEqual(self.db.cacheDetailSize(), [])
 
         CACHE_SIZE = 10
         self.db.setCacheSize(CACHE_SIZE)
@@ -444,6 +444,7 @@ def test_basic_cache_size_estimation():
     >>> import ZODB.MappingStorage
     >>> db = ZODB.MappingStorage.DB()
     >>> conn = db.open()
+    >>> conn.cacheMinimize() # See fix84.rst
 
     >>> def check_cache_size(cache, expected):
     ...     actual = cache.total_estimated_size

src/ZODB/tests/testConnection.py

@@ -230,6 +230,7 @@ def doctest_get(self):
 
         >>> db = databaseFromString("<zodb>\n<mappingstorage/>\n</zodb>")
         >>> cn = db.open()
+        >>> cn.cacheMinimize() # See fix84.rst
         >>> obj = cn.get(p64(0))
         >>> obj._p_oid
         '\x00\x00\x00\x00\x00\x00\x00\x00'

src/ZODB/tests/testDB.py

@@ -125,7 +125,7 @@ def connectionDebugInfo():
     r"""DB.connectionDebugInfo provides information about connections.
 
     >>> import time
-    >>> now = 1228423244.5
+    >>> now = 1228423244.1
     >>> def faux_time():
     ...     global now
     ...     now += .1
@@ -154,8 +154,8 @@ def connectionDebugInfo():
     >>> before = [x['before'] for x in info]
     >>> opened = [x['opened'] for x in info]
     >>> infos = [x['info'] for x in info]
-    >>> before
-    [None, '\x03zY\xd8\xc0m9\xdd', None]
+    >>> before == [None, c1.root()._p_serial, None]
+    True
     >>> opened
     ['2008-12-04T20:40:44Z (1.30s)', '2008-12-04T20:40:46Z (0.10s)', None]
     >>> infos
@@ -351,6 +351,7 @@ def minimally_test_connection_timeout():
 
     >>> db = ZODB.DB(None, pool_timeout=.01)
     >>> c1 = db.open()
+    >>> c1.cacheMinimize() # See fix84.rst
     >>> c2 = db.open()
     >>> c1.close()
     >>> c2.close()