X Stub ZODB/persistent/BTrees/ZEO have to be installed manually for forward-compatibility with ZODB4 and ZODB5

Else installing any egg that depends on 'ZODB' (not 'ZODB3') will pull
in ZODB5. Example of those eggs are zodbtools, zodburi, ...

[ This is ZODB3 backport of commit bb9bf539
  (https://github.com/zopefoundation/ZODB/pull/298) ]

ZODB tries to avoid saving empty transactions to storage on
`transaction.commit()`. The way it works is: if no objects were changed
during ongoing transaction, ZODB.Connection does not join current
TransactionManager, and transaction.commit() performs two-phase commit
protocol only on joined DataManagers. In other words if no objects were
changed, no tpc_*() methods are called at all on ZODB.Connection at
transaction.commit() time.

This way application servers like Zope/ZServer/ERP5/... can have
something as

    try:
        # process incoming request
        transaction.commit()    # processed ok
    except:
        transaction.abort()
        # problem: log + reraise

in top-level code to process requests without creating many on-disk
transactions with empty data changes just because read-only requests
were served.

Everything is working as intended.

However at storage level, FileStorage currently also checks whether
transaction that is being committed also comes with empty data changes,
and _skips_ saving transaction into disk *at all* for such cases, even
if it has been explicitly told to commit the transaction via two-phase
commit protocol calls done at storage level.

This creates the situation, where contrary to promise in
ZODB/interfaces.py(*), after successful tpc_begin/tpc_vote/tpc_finish()
calls made at storage level, transaction is _not_ made permanent,
despite tid of "committed" transaction being returned to caller. In other
words FileStorage, when asked to commit a transaction, even if one with
empty data changes, reports "ok" and gives transaction ID to the caller,
without creating corresponding transaction record on disk.

This behaviour is

a) redundant to application-level avoidance to create empty transaction
   on storage described in the beginning, and

b) creates problems:

The first problem is that application that works at storage-level might
be interested in persisting transaction, even with empty changes to
data, just because it wants to save the metadata similarly to e.g.
`git commit --allow-empty`.

The other problem is that an application view and data in database
become inconsistent: an application is told that a transaction was
created with corresponding transaction ID, but if the storage is
actually inspected, e.g. by iteration, the transaction is not there.
This, in particular, can create problems if TID of committed transaction
is reported elsewhere and that second database client does not find the
transaction it was told should exist.

I hit this particular problem with wendelin.core. In wendelin.core,
there is custom virtual memory layer that keeps memory in sync with
data in ZODB. At commit time, the memory is inspected for being dirtied,
and if a page was changed, virtual memory layer joins current
transaction _and_ forces corresponding ZODB.Connection - via which it
will be saving data into ZODB objects - to join the transaction too,
because it would be too late to join ZODB.Connection after 2PC process
has begun(+). One of the format in which data are saved tries to
optimize disk space usage, and it actually might happen, that even if
data in RAM were dirtied, the data itself stayed the same and so nothing
should be saved into ZODB. However ZODB.Connection is already joined
into transaction and it is hard not to join it because joining a
DataManager when the 2PC is already ongoing does not work.

This used to work ok with wendelin.core 1, but with wendelin.core 2 -
where separate virtual filesystem is also connected to the database to
provide base layer for arrays mappings - this creates problem, because
when wcfs (the filesystem) is told to synchronize to view the database
@tid of committed transaction, it can wait forever waiting for that, or
later, transaction to appear on disk in the database, creating
application-level deadlock.

I agree that some more effort might be made at wendelin.core side to
avoid committing transactions with empty data at storage level.

However the most clean way to fix this problem in my view is to fix
FileStorage itself, because if at storage level it was asked to commit
something, it should not silently skip doing so and dropping even non-empty
metadata + returning ok and committed transaction ID to the caller.

As described in the beginning this should not create problems for
application-level ZODB users, while at storage-level the implementation
is now consistently matching interface and common sense.

----

(*) tpc_finish: Finish the transaction, making any transaction changes permanent.
    Changes must be made permanent at this point.
    ...

    https://github.com/zopefoundation/ZODB/blob/5.5.1-35-gb5895a5c2/src/ZODB/interfaces.py#L828-L831

(+) https://lab.nexedi.com/kirr/wendelin.core/blob/9ff5ed32/bigfile/file_zodb.py#L788-822

----

kirr: This is likely to be ZODB3-backport of https://github.com/zopefoundation/ZODB/pull/69
Taken from https://lab.nexedi.com/nexedi/neoppod/blob/v1.12-52-gfb746e6b/ZODB3.patch

People say that ZODB3 is kind of closed:

	https://github.com/zopefoundation/ZODB/pull/306#issuecomment-606735225

Givent that even for ZEO4 we were suggested that 4 is considered "dead" by upstream:

	https://github.com/zopefoundation/ZEO/pull/161#pullrequestreview-447245642

Let's keep on patching ZODB3 in our local fork until we keep on using it.

Changes are backported from commits 227953b9
and 03a326be.

( This is backport of https://github.com/zopefoundation/persistent/pull/44
  to ZODB-3.10 )

On ._p_deactivate() and ._p_invalidate(), when an object goes to ghost
state, objects referenced by all its attributes, except related to
persistence machinery, are released, this way freeing memory (if they
were referenced only from going-to-ghost object).

That's the idea - an object in ghost state is simply a stub, which loads
its content on first access (via hooking into get/set attr) while
occupying minimal memory in not-yet-loaded state.

However the above is not completely true right now, as currently on
ghostification only object's .__dict__ is released, while in-slots objects
are retained attached to ghost object staying in RAM:

    ---- 8< ----
    from ZODB import DB
    from persistent import Persistent
    import gc

    db = DB(None)
    jar = db.open()

    class C:
        def __init__(self, v):
            self.v = v
        def __del__(self):
            print 'released (%s)' % self.v

    class P1(Persistent):
        pass

    class P2(Persistent):
        __slots__ = ('aaa')

    p1 = P1()
    jar.add(p1)
    p1.aaa = C(1)

    p2 = P2()
    jar.add(p2)
    p2.aaa = C(2)

    p1._p_invalidate()
    # "released (1)" is printed

    p2._p_invalidate()
    gc.collect()
    # "released (2)" is NOT printed     <--
    ---- 8< ----

So teach ghostify() & friends to release objects in slots to free-up
memory when an object goes to ghost state.

NOTE PyErr_Occurred() added after ghostify() calls because
pickle_slotnames() can raise an error, but we do not want to change
ghostify() prototype for backward compatibility reason - as it is used
in cPersistenceCAPIstruct.

( I hit this bug with wendelin.core which uses proxies to load
  data from DB to virtual memory manager and then deactivate proxy right
  after load has been completed:

  https://lab.nexedi.com/nexedi/wendelin.core/blob/f7803634/bigfile/file_zodb.py#L239
  https://lab.nexedi.com/nexedi/wendelin.core/blob/f7803634/bigfile/file_zodb.py#L295 )

This reverts to the behaviour of 3.10.3 and older.

(cherry picked from commit b74eef76)

Conflicts:
	src/ZODB/tests/testconflictresolution.py

Multi-threaded IO support, which is new to ZODB 3.10, allows clients to read
data (load & loadBefore) even after tpc_vote has started to write a new
transaction to disk. This is done by using different 'file' objects.

Issues start when a transaction is rolled back after data has been appended
(using the writing file object). Truncating is not enough because the FilePool
may have been used concurrently to read the end of the last transaction:
file objects have their own read buffers which, in this case, may also contain
the beginning of the aborted transaction.

So a solution is to invalidate read buffers whenever they may contain wrong
data. This patch does it on truncation, which happens rarely enough to not
affect performance.

We discovered this bug in the following conditions:
- ZODB splitted in several FileStorage
- many conflicts in the first committed DB, but always resolved
- unresolved conflict in another DB
If the transaction is replayed with success (no more conflict in the other DB),
a subsequent load of the object that could be resolved in the first DB may, for
example, return a wrong serial (tid of the aborted transaction) if the layout
of the committed transaction matches that of the aborted one.

The bug usually manifests with POSKeyError & CorruptedDataError exceptions in
ZEO logs, for example while trying to resolve a conflict (and restarting the
transaction does not help, causing Site Errors in Zope). But theorically,
this could also cause silent corruption or unpickling errors at client side.

(cherry picked from commit 028b1922)

Conflicts:
	src/ZODB/FileStorage/FileStorage.py

Fixing uncaught exception problem on shutdown

Nested connections try to clean up themselves multiple
times. This does not work

see https://github.com/zopefoundation/ZODB/issues/16

see https://github.com/zopefoundation/ZODB/issues/16