neoctl gets a new command to change the number of replicas.

The number of replicas becomes a new partition table attribute and
like the PT id, it is stored in the config table. On the other side,
the configuration value for the number of partitions is dropped,
since it can be computed from the partition table, which is
always stored in full.

The -p/-r master options now only apply at database creation.

Some implementation notes:

- The protocol is slightly optimized in that the master now sends
  automatically the whole partition tables to the admin & client
  nodes upon connection, like for storage nodes.
  This makes the protocol more consistent, and the master is the
  only remaining node requesting partition tables, during recovery.

- Some parts become tricky because app.pt can be None in more cases.
  For example, the extra condition in NodeManager.update
  (before app.pt.dropNode) was added for this is the reason.
  Or the 'loadPartitionTable' method (storage) that is not inlined
  because of unit tests.
  Overall, this commit simplifies more than it complicates.

- In the master handlers, we stop hijacking the 'connectionCompleted'
  method for tasks to be performed (often send the full partition
  table) on handler switches.

- The admin's 'bootstrapped' flag could have been removed earlier:
  race conditions can't happen since the AskNodeInformation packet
  was removed (commit d048a52d).

It is often faster to set up replicas by stopping a node (and any
underlying database server like MariaDB) and do a raw copy of the
database (e.g. with rsync). So far, it required to stop the whole
cluster and use tools like 'mysql' or sqlite3' to edit:
- the 'pt' table in databases,
- the 'config.nid' values of the new nodes.

With this new option, if you already have 1 replica, you can set up
new replicas with such fast raw copy, and without interruption of
service. Obviously, this implies less redundancy during the operation.

This is not used currently.

This breaks compatibily but it was mentionned from the beginning
that these options are only there for testing purpose.

TODO: rename all remaining occurrences of UUID into NID in the code

If the source DB is lost during the import and then restored from a backup,
all new transactions have to written back again on resume. It is the most
common case for which the writeback hits the maximum number of transactions
per partition to process at each iteration; the previous code was buggy in
that it could skip transactions.

Example output:

    stress: yes (toggle with F1)
    cluster state: RUNNING
    last oid: 0x44c0
    last tid: 0x3cdee272ef19355 (2019-02-26 15:35:11.002419)
    clients: 2308, 2311, 2302, 2173, 2226, 2215, 2306, 2255, 2314, 2356 (+48)
            8m53.988s (42.633861/s)
    pt id: 4107
        RRRDDRRR
     0: OU......
     1: ..UO....
     2: ....OU..
     3: ......UU
     4: OU......
     5: ..UO....
     6: ....OU..
     7: ......UU
     8: OU......
     9: ..UO....
    10: ....OU..
    11: ......UU
    12: OU......
    13: ..UO....
    14: ....OU..
    15: ......UU
    16: OU......
    17: ..UO....
    18: ....OU..
    19: ......UU
    20: OU......
    21: ..UO....
    22: ....OU..
    23: ......UU

getAddress (via __repr__) raised EBADF on closed connectors.

In functional tests (or anything reusing this framework),
the mapping could be incorrect at the beginning of logs.

Corrupted logs cause neolog to fail with the following error:

  AttributeError: 'Log' object has no attribute 'uuid_str'

This makes commit 3c7a3160
(storage: speed up reads by indexing 'obj' primarily by 'oid')
effective for SQLite.

The fake changes in test data are because we don't force upgrade
for this optimization.

Commit aa4d621d broke log rotation
and neolog sometimes failed to read in new format.

neolog has new options: -N for old behaviour, and -C to show the cluster name.

Since commit 50e7fe52,
some code can be simplified.

This fixes a bug that could manifest as follows:

  Traceback (most recent call last):
    File "neo/client/app.py", line 432, in load
      self._cache.store(oid, data, tid, next_tid)
    File "neo/client/cache.py", line 223, in store
      assert item.tid == tid, (item, tid)
  AssertionError: (<CacheItem oid='\x00\x00\x00\x00\x00\x00\x00\x01' tid='\x03\xcb\xc6\xca\xfd\xc7\xda\xee' next_tid='\x03\xcb\xc6\xca\xfd\xd8\t\x88' data='...' counter=1 level=1 expire=10000 prev=<...> next=<...>>, '\x03\xcb\xc6\xca\xfd\xd8\t\x88')

The big changes in the threaded test framework are required because we need to
reproduce a race condition between client threads and this conflicts with the
serialization of epoll events (deadlock).

This was found when stress-testing a big cluster. 1 client node was stuck:

  (Pdb) pp app.dispatcher.__dict__
  {'lock_acquire': <built-in method acquire of thread.lock object at 0x7f788c6e4250>,
  'lock_release': <built-in method release of thread.lock object at 0x7f788c6e4250>,
  'message_table': {140155667614608: {},
                    140155668875280: {},
                    140155671145872: {},
                    140155672381008: {},
                    140155672381136: {},
                    140155672381456: {},
                    140155673002448: {},
                    140155673449680: {},
                    140155676093648: {170: <neo.lib.locking.SimpleQueue object at 0x7f788a109c58>},
                    140155677536464: {},
                    140155679224336: {},
                    140155679876496: {},
                    140155680702992: {},
                    140155681851920: {},
                    140155681852624: {},
                    140155682773584: {},
                    140155685988880: {},
                    140155693061328: {},
                    140155693062224: {},
                    140155693074960: {},
                    140155696334736: {278: <neo.lib.locking.SimpleQueue object at 0x7f788a109c58>},
                    140155696411408: {},
                    140155696414160: {},
                    140155696576208: {},
                    140155722373904: {}},
  'queue_dict': {140155673622936: 1, 140155689147480: 2}}

140155673622936 should not be queue_dict

The idea is to write:

  with self.expectedFailure(...): \

just before the statement that is expected to fail. Contrary to the existing
decorator, we want to:
- be sure that the test fails at the expected line;
- be able to remove an expectedFailure without touching the code around.

When ConnectionPool._initNodeConnection fails a first time with:

  StorageError: protocol error: already connected

the following assertion failure happens when trying to reconnect before the
previous connection is actually closed (currently, only the node sending an
error message closes the connection, as commented in EventHandler):

  Traceback (most recent call last):
    File "neo/client/Storage.py", line 82, in load
      return self.app.load(oid)[:2]
    File "neo/client/app.py", line 367, in load
      data, tid, next_tid, _ = self._loadFromStorage(oid, tid, before_tid)
    File "neo/client/app.py", line 399, in _loadFromStorage
      askStorage)
    File "neo/client/app.py", line 293, in _askStorageForRead
      conn = cp.getConnForNode(node)
    File "neo/client/pool.py", line 98, in getConnForNode
      conn = self._initNodeConnection(node)
    File "neo/client/pool.py", line 48, in _initNodeConnection
      dispatcher=app.dispatcher)
    File "neo/lib/connection.py", line 704, in __init__
      super(MTClientConnection, self).__init__(*args, **kwargs)
    File "neo/lib/connection.py", line 602, in __init__
      node.setConnection(self)
    File "neo/lib/node.py", line 122, in setConnection
      attributeTracker.whoSet(self, '_connection'))
  AssertionError

This fixes:

  Traceback (most recent call last):
    File "neo/client/Storage.py", line 108, in tpc_vote
      return self.app.tpc_vote(transaction)
    File "neo/client/app.py", line 546, in tpc_vote
      self.waitStoreResponses(txn_context)
    File "neo/client/app.py", line 539, in waitStoreResponses
      _waitAnyTransactionMessage(txn_context)
    File "neo/client/app.py", line 160, in _waitAnyTransactionMessage
      self._handleConflicts(txn_context)
    File "neo/client/app.py", line 514, in _handleConflicts
      self._store(txn_context, oid, serial, data)
    File "neo/client/app.py", line 452, in _store
      self._waitAnyTransactionMessage(txn_context, False)
    File "neo/client/app.py", line 155, in _waitAnyTransactionMessage
      self._waitAnyMessage(queue, block=block)
    File "neo/client/app.py", line 142, 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 143, in answerRebaseObject
      assert cached == data
  AssertionError

During rebase, writes could stay lockless although the partition was
replicated. Another transaction could then take locks prematurely, leading to
the following crash:

  Traceback (most recent call last):
    File "neo/lib/handler.py", line 72, in dispatch
      method(conn, *args, **kw)
    File "neo/storage/handlers/master.py", line 36, in notifyUnlockInformation
      self.app.tm.unlock(ttid)
    File "neo/storage/transactions.py", line 329, in unlock
      self.abort(ttid, even_if_locked=True)
    File "neo/storage/transactions.py", line 573, in abort
      not self._replicated.get(self.getPartition(oid))), x
  AssertionError: ('\x00\x00\x00\x00\x00\x03\x03v', '\x03\xca\xb44J\x13\x99\x88', '\x03\xca\xb44J\xe0\xdcU', {}, set(['\x00\x00\x00\x00\x00\x03\x03v']))

Flushing logs will help fixing NEO bugs (e.g. failed assertions).

This fixes:

  Traceback (innermost last):
    ...
    Module transaction._transaction, line 393, in _commitResources
      rm.tpc_vote(self)
    Module ZODB.Connection, line 797, in tpc_vote
      s = vote(transaction)
    Module neo.client.Storage, line 95, in tpc_vote
      return self.app.tpc_vote(transaction)
    Module neo.client.app, line 546, in tpc_vote
      self.waitStoreResponses(txn_context)
    Module neo.client.app, line 539, in waitStoreResponses
      _waitAnyTransactionMessage(txn_context)
    Module neo.client.app, line 160, in _waitAnyTransactionMessage
      self._handleConflicts(txn_context)
    Module neo.client.app, line 471, in _handleConflicts
      assert oid is None, (oid, serial)
  AssertionError: ('\x00\x00\x00\x00\x00\x02\n\xe3', '\x03\xca\xad\xcb!\x92\xb6\x9c')

With previous commit, there's no point anymore to distinguish storage nodes
for which we only check serials.

Not doing so was an incorrect optimization. Checking serials does take
write-locks and they must not be released when a client-storage connection
breaks between vote and lock, otherwise a concurrent transaction modifying such
serials may finish before.