Made neoctl ... print ids more understandable with the unpackTID function (it now prints date and time, as well as the hex values for backup_tid and last_tid)

Many patches have been merged upstream :)

A notable change is that lastTransaction() does not ping the master anymore
(but it still causes a connection to the master if the client is disconnected).

After partitions were dropped with TokuDB, we had a case where MariaDB 10.1.14
stopped using the most appropriate index.

MariaDB [neo0]> explain SELECT DISTINCT data_id FROM obj WHERE `partition`=5;
+------+-------------+-------+-------+-------------------+---------+---------+------+------+---------------------------------------+
| id   | select_type | table | type  | possible_keys     | key     | key_len | ref  | rows | Extra                                 |
+------+-------------+-------+-------+-------------------+---------+---------+------+------+---------------------------------------+
|    1 | SIMPLE      | obj   | range | PRIMARY,partition | data_id | 11      | NULL |   10 | Using where; Using index for group-by |
+------+-------------+-------+-------+-------------------+---------+---------+------+------+---------------------------------------+
MariaDB [neo0]> SELECT SQL_NO_CACHE DISTINCT data_id FROM obj WHERE `partition`=5;
Empty set (1 min 51.47 sec)

Expected:

MariaDB [neo1]> explain SELECT DISTINCT data_id FROM obj WHERE `partition`=4;
+------+-------------+-------+------+-------------------+---------+---------+-------+------+------------------------------+
| id   | select_type | table | type | possible_keys     | key     | key_len | ref   | rows | Extra                        |
+------+-------------+-------+------+-------------------+---------+---------+-------+------+------------------------------+
|    1 | SIMPLE      | obj   | ref  | PRIMARY,partition | PRIMARY | 2       | const |    1 | Using where; Using temporary |
+------+-------------+-------+------+-------------------+---------+---------+-------+------+------------------------------+
1 row in set (0.00 sec)
MariaDB [neo1]> SELECT SQL_NO_CACHE DISTINCT data_id FROM obj WHERE `partition`=4;
Empty set (0.00 sec)

Restarting the server or 'OPTIMIZE TABLE obj; ' does not help.

Such issue could prevent the cluster to start due to timeouts, by always going
back to RECOVERING state.

Freeing disk space when a cell is dropped will have to be implemented with care,
not only for performance reasons.

TRUNCATE was chosen for performance reasons, but it's usually done on small
tables, and not for performance-critical operations. TRUNCATE commits
implicitely, so for pt/ttrans in particular, it's certainly slower due to extra
fsyncs to disk.

On the other side, committing too early can corrupt the database if the storage
node is stopped just after. For example, a failure in changePartitionTable()
can cause 'pt' to remain empty.

It slowed down everything but abortFor(), which is not performance critical.

This reverts commit 7aecdada partially.
There seems to be no bug here, because:
- abortFor() is only called upon a notification from the master that a client
  is disconnected,
- and from the same TCP connection, we only receive a LockInformation packet
  if there's still such a transaction on the master side.

The code removed in abortFor() was redundant with abort().

There was a bug that connections were not maintained during a TPC,
which caused transactions to be aborted when the limit was reached.

Given that oids are spreaded evenly over all partitions, and that clients always
write to all cells of each involved partitions, clients would spend their time
reconnecting to storage nodes as soon as the limit is reached. So such feature
really looks counter-productive.

Client nodes ignored the state of the connection to the master node when reading
data from storage, as long as their partition tables were recent enough. This
way, they were able to finish read-only transactions even if they could't reach
the master, which could be useful for high availability. The downside is that
the master node ignored that their node ids were still used, which causes "uuid"
conflicts when reallocating them.

Rejected solutions:
- An unused NEO Storage should not insist in staying connected to master node.
- Reverting to big random node identifiers is a lot of work and it would make
  debugging annoying (see commit 23fad3af).
- Always increasing node ids could have been a simple solution if we accepted
  that the cluster dies after that all 2^24 possible ids were allocated.

Given that reading from storage without being connected to the master can only
be useful to finish the current transaction (because we always ping the master
at the beginning of every transaction), keeping such feature is not worth the
effort.

This commit fixes id conflicts in a very simple way, by clearing the partition
table upon primary node failure, which forces reconnection to the master before
querying any storage node. In such case, we raise a special exception that will
cause the transaction to be restarted, so that the user does not get errors for
temporary connection failures.

Currently, another argument not to lock is that we would not be able to test
incremental resolution anymore. We can think about this again when deadlock
resolution is implemented.

The following error was reported on a client node:

    #0x0000 Error                   < None (2001:...:2051)
    1 (Retry Later)
    connection closed for <MTClientConnection(uuid=None, address=2001:...:2051, handler=PrimaryNotificationsHandler, closed, client) at 7f1ea7c42f90>
    Event Manager:
    connection started for <MTClientConnection(uuid=None, address=2001:...:2051, handler=PrimaryNotificationsHandler, fd=13, on_close=onConnectionClosed, connecting, client) at 7f1ea7c25c10>
    #0x0000 RequestIdentification          > None (2001:...:2051)
      Readers: []
      Writers: []
      Connections:
        13: <MTClientConnection(uuid=None, address=2001:...:2051, handler=PrimaryNotificationsHandler, fd=13, on_close=onConnectionClosed, connecting, client) at 7f1ea7c25c10> (pending=False)
    Node manager : 1 nodes
    * None |   MASTER | 2001:...:2051 | UNKNOWN
    <ClientCache history_size=0 oid_count=0 size=0 time=0 queue_length=[0] (life_time=10000 max_history_size=100000 max_size=20971520)>
    poll raised, retrying
    Traceback (most recent call last):
      File "neo/lib/threaded_app.py", line 93, in _run
        poll(1)
      File "neo/lib/event.py", line 134, in poll
        self._poll(0)
      File "neo/lib/event.py", line 164, in _poll
        conn = self.connection_dict[fd]
    KeyError: 13

which means that:
- while the poll thread is getting a (13, EPOLLIN) event because it is
  closed (aborted by the master)
- another thread processes the error packet, by closing it in
  PrimaryBootstrapHandler.notReady
- next, the poll thread resumes the execution of EpollEventManager._poll
  and fails to find fd=13 in self.connection_dict

So here, we have a race condition between epoll_wait and any further use
of connection_dict to map returned fds.

However, what commit a4731a0c does to handle
the case of fd reallocation only works for mono-threaded applications.
In EPOLLIN, wrapping 'self.connection_dict[fd]' the same way as for other
events is not enough. For example:
- case 1:
  - thread 1: epoll returns fd=13
  - thread 2: close(13)
  - thread 2: open(13)
  - thread 1: self.connection_dict[13] does not match
              but this would be handled by the 'unregistered' list
- case 2:
  - thread 1: reset 'unregistered'
  - thread 2: close(13)
  - thread 2: open(13)
  - thread 1: epoll returns fd=13
  - thread 1: self.connection_dict[13] matches
              but it would be wrongly ignored by 'unregistered'
- case 3:
  - thread 1: about to call readable/writable/onTimeout on a connection
  - thread 2: this connection is closed
  - thread 1: readable/writable/onTimeout wrongly called on a closed connection

We could protect _poll() with a lock, and make unregister() use wakeup() so
that it gets a chance to acquire it, but that causes threaded tests to deadlock
(continuing in this direction seems too complicated).

So we have to deal with the fact that there can be race conditions at any time
and there's no way to make 'connection_dict' match exactly what epoll returns.
We solve this by preventing fd reallocation inside _poll(), which is fortunately
possible with sockets, using 'shutdown': the closing of fds is delayed.

For above case 3, readable/writable/onTimeout for MTClientConnection are also
changed to test whether the connection is still open while it has the lock.
Just for safety, we do the same for 'process'.

At last, another kind of race condition that this commit also fixes concerns
the use of itervalues() on EventManager.connection_dict.

This is a preliminary commit, without any functional change,
just to make the next one easier to review.

We already have logs when a connection fails,
and ask() raises ConnectionClosed if the connection is closed.

SourceForge currently has too many issues.

Obviously, oids can't be automatically invalidated if the undo is done directly
at the storage level.

In commit 9cca0f8e, only 1 bug was found.

FileStorage has been fixed in commit b7ea4e6f708dcded329332b24a9d70211a6b6368

Cache items are stored in double-linked chains. In order to quickly know the
number of history items, an extra attribute is used to count them. It was not
always decremented when a history item was removed.

This led to the following exception:
  <ClientCache history_size=100000 oid_count=1959 size=20970973 time=2849049 queue_length=[1, 7, 738, 355, 480, 66, 255, 44, 3, 5, 2, 1, 3, 4, 2, 2] (life_time=10000 max_history_size=100000 max_size=20971520)>
  poll raised, retrying
  Traceback (most recent call last):
    ...
    File "neo/client/handlers/master.py", line 137, in packetReceived
      cache.store(oid, data, tid, None)
    File "neo/client/cache.py", line 247, in store
      self._add(head)
    File "neo/client/cache.py", line 129, in _add
      self._remove(head)
    File "neo/client/cache.py", line 136, in _remove
      level = item.level
  AttributeError: 'NoneType' object has no attribute 'level'

This fixes the following issue:

WARNING replication aborted for partition 1
DEBUG   connection started for <ClientConnection(uuid=None, address=...:43776, handler=StorageOperationHandler, fd=10, on_close=onConnectionClosed, connecting, client) at 7f5d2067fdd0>
DEBUG   connect failed for <SocketConnectorIPv6 at 0x7f5d2067fe10 fileno 10 ('::', 0), opened to ('...', 43776)>: ENETUNREACH (Network is unreachable)
WARNING replication aborted for partition 5
DEBUG   connection started for <ClientConnection(uuid=None, address=...:43776, handler=StorageOperationHandler, fd=10, on_close=onConnectionClosed, connecting, client) at 7f5d1c409510>
PACKET  #0x0000 RequestIdentification          > None (...:43776)  | (<EnumItem STORAGE (1)>, None, ('...', 60533), '...')
ERROR   Pre-mortem data:
ERROR   Traceback (most recent call last):
ERROR     File "neo/storage/app.py", line 157, in run
ERROR       self._run()
ERROR     File "neo/storage/app.py", line 197, in _run
ERROR       self.doOperation()
ERROR     File "neo/storage/app.py", line 285, in doOperation
ERROR       poll()
ERROR     File "neo/storage/app.py", line 95, in _poll
ERROR       self.em.poll(1)
ERROR     File "neo/lib/event.py", line 121, in poll
ERROR       self._poll(blocking)
ERROR     File "neo/lib/event.py", line 165, in _poll
ERROR       if conn.readable():
ERROR     File "neo/lib/connection.py", line 481, in readable
ERROR       self._closure()
ERROR     File "neo/lib/connection.py", line 539, in _closure
ERROR       self.close()
ERROR     File "neo/lib/connection.py", line 531, in close
ERROR       handler.connectionClosed(self)
ERROR     File "neo/lib/handler.py", line 135, in connectionClosed
ERROR       self.connectionLost(conn, NodeStates.TEMPORARILY_DOWN)
ERROR     File "neo/storage/handlers/storage.py", line 59, in connectionLost
ERROR       replicator.abort()
ERROR     File "neo/storage/replicator.py", line 339, in abort
ERROR       self._nextPartition()
ERROR     File "neo/storage/replicator.py", line 260, in _nextPartition
ERROR       None if name else app.uuid, app.server, name or app.name))
ERROR     File "neo/lib/connection.py", line 562, in ask
ERROR       raise ConnectionClosed
ERROR   ConnectionClosed

This fixes a lock leak on storages, causing further transactions to timeout.