Traceback (most recent call last):
  ...
  File "neo/lib/handler.py", line 72, in dispatch
    method(conn, *args, **kw)
  File "neo/master/handlers/client.py", line 70, in askFinishTransaction
    conn.getPeerId(),
  File "neo/master/transactions.py", line 387, in prepare
    assert node_list, (ready, failed)
AssertionError: (set([]), frozenset([]))

Master log leading to the crash:
  PACKET    #0x0009 StartOperation                 > S1
  PACKET    #0x0004 BeginTransaction               < C1
  DEBUG     Begin <...>
  PACKET    #0x0004 AnswerBeginTransaction         > C1
  PACKET    #0x0001 NotifyReady                    < S1

It was wrong to process BeginTransaction before receiving NotifyReady.

The changes in the storage are cosmetics: the 'ready' attribute has become
redundant with 'operational'.

Due to a bug in MariaDB Connector/C 2.3.2, some tests like testBasicStore and
test_max_allowed_packet were retrying the same failing query indefinitely.

On clusters with many deadlock avoidances, this flooded logs.
Hopefully, this commit reduces the size of logs without losing information.

An issue that happened for the first time on a storage node didn't always cause
other nodes to flush their logs, which made debugging difficult.

Generators are not thread-safe:

Exception in thread T2:
Traceback (most recent call last):
  ...
  File "ZODB/tests/StorageTestBase.py", line 157, in _dostore
    r2 = self._storage.tpc_vote(t)
  File "neo/client/Storage.py", line 95, in tpc_vote
    return self.app.tpc_vote(transaction)
  File "neo/client/app.py", line 507, in tpc_vote
    self.waitStoreResponses(txn_context)
  File "neo/client/app.py", line 500, in waitStoreResponses
    _waitAnyTransactionMessage(txn_context)
  File "neo/client/app.py", line 145, in _waitAnyTransactionMessage
    self._waitAnyMessage(queue, block=block)
  File "neo/client/app.py", line 128, in _waitAnyMessage
    conn, packet, kw = get(block)
  File "neo/lib/locking.py", line 203, in get
    self._lock()
  File "neo/tests/threaded/__init__.py", line 590, in _lock
    for i in TIC_LOOP:
ValueError: generator already executing

======================================================================
FAIL: check_checkCurrentSerialInTransaction (neo.tests.zodb.testBasic.BasicTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "neo/tests/zodb/testBasic.py", line 33, in check_checkCurrentSerialInTransaction
    super(BasicTests, self).check_checkCurrentSerialInTransaction()
  File "ZODB/tests/BasicStorage.py", line 294, in check_checkCurrentSerialInTransaction
    utils.load_current(self._storage, b'\0\0\0\0\0\0\0\xf4')[1])
failureException: False is not true

This is done by moving
        self.replicator.populate()
after the switch to MasterOperationHandler, so that the latter is not delayed.

This change comes with some refactoring of the main loop,
to clean up app.checker and app.replicator properly (like app.tm).

Another option could have been to process notifications with the last handler,
instead of the first one. But if possible, cleaning up the whole code to not
delay handlers anymore looks the best option.

This happened in 2 cases:
- Commit a4c06242 ("Review aborting of
  transactions") introduced a race condition causing oids to remain
  write-locked forever after that the transaction modifying them is aborted.
- An unfinished transaction is not locked/unlocked during tpc_finish: oids
  must be unlocked when being notified that the transaction is finished.

This was found by the first assertion of answerRebaseObject (client) because
a storage node missed a few transactions and reported a conflict with an older
serial than the one being stored: this must never happen and this commit adds a
more generic assertion on the storage side.

The above case is when the "first phase" of replication of a partition
(all history up to the tid before unfinished transactions) ended after
that the unfinished transactions are finished: this was a corruption bug,
where UP_TO_DATE cells could miss data.

Otherwise, if the "first phase" ended before, then the partition remained stuck
in OUT_OF_DATE state. Restarting the storage node was enough to recover.

Traceback (most recent call last):
  ...
  File "neo/client/app.py", line 507, in tpc_vote
    self.waitStoreResponses(txn_context)
  File "neo/client/app.py", line 500, in waitStoreResponses
    _waitAnyTransactionMessage(txn_context)
  File "neo/client/app.py", line 150, in _waitAnyTransactionMessage
    self._handleConflicts(txn_context)
  File "neo/client/app.py", line 474, in _handleConflicts
    self._store(txn_context, oid, conflict_serial, data)
  File "neo/client/app.py", line 410, in _store
    self._waitAnyTransactionMessage(txn_context, False)
  File "neo/client/app.py", line 145, in _waitAnyTransactionMessage
    self._waitAnyMessage(queue, block=block)
  File "neo/client/app.py", line 133, in _waitAnyMessage
    _handlePacket(conn, packet, kw)
  File "neo/lib/threaded_app.py", line 133, in _handlePacket
    handler.dispatch(conn, packet, kw)
  File "neo/lib/handler.py", line 72, in dispatch
    method(conn, *args, **kw)
  File "neo/client/handlers/storage.py", line 122, in answerRebaseObject
    assert txn_context.conflict_dict[oid] == (serial, conflict)
AssertionError

Scenario:
0. unanswered rebase from S2
1. conflict resolved between t1 and t2 -> S1 & S2
2. S1 reports a new conflict
3. S2 answers to the rebase:
   returned serial (t1) is smaller than in conflict_dict (t2)
4. S2 reports the same conflict as in 2

Traceback (most recent call last):
  ...
  File "neo/storage/handlers/storage.py", line 111, in answerFetchObjects
    self.app.replicator.finish()
  File "neo/storage/replicator.py", line 370, in finish
    self._nextPartition()
  File "neo/storage/replicator.py", line 279, in _nextPartition
    assert app.pt.getCell(offset, app.uuid).isOutOfDate()
AssertionError

The scenario is:
1. partition A: start of replication, with unfinished transactions
2. partition A: all unfinished transactions are finished
3. partition A: end of replication with ReplicationDone notification
4. replication of partition B
5. partition A: AssertionError when starting replication

The bug is that in 3, the partition A is partially replicated and the storage
node must not notify the master.

This fixes testBasicStore when run with MySQL backend, which started to fail
with commit 9eb06ff1 when -L runner option is
not used.

This is a first version with several optimizations possible:
- improve EventQueue (or implement a specific queue) to minimize deadlocks
- turn the RebaseObject packet into a notification

Sorting oids could also be useful to reduce the probability of deadlocks,
but that would never be enough to avoid them completely, even if there's a
single storage. For example:

1. C1 does a first store (x or y)
2. C2 stores x and y; one is delayed
3. C1 stores the other -> deadlock
   When solving the deadlock, the data of the first store may only
   exist on the storage.

2 functional tests are removed because they're redundant,
either with ZODB tests or with the new threaded tests.

- Make sure that errors while processing a delayed packet are reported to the
  connection that sent this packet.
- Provide a mechanism to process events for the same connection in
  chronological order.

Fix conflict handling after a successful store to a node being disconnected for having missed a transaction

- fail sooner in case of unresolvable conflict
- avoid OOM when there are many conflicts

Now that we do inequality comparisons between timestamps, the master must
use a monotonic clock, to avoid issues when the clock is turned back.
Before, the probability that time.time() returned again the same value was
probably negligible.

This optimizes the normal case, and handlers can now take specific action
when requests are cancelled because a connection is closed.