- mention in comments that _ZBigFileH not only proxies changes from
  virtmem -> ZODB, but also the other way: virtmem <- ZODB.
- refresh comments, fix typo.

It was from long-ago marked as "XXX move to common place".

I noticed this while working on WCFS: if file blocks topology change,
the invalidation process is not working correctly. It is also not
correct with respect to live cache pressure.

Add FIXME in the code and test for live cache pressure.

kirr/wendelin.core@5a4562fc
kirr/wendelin.core@48eb692f
kirr/wendelin.core@d1a579b2
kirr/wendelin.core@69c94fbc

For ZBlk0 this is trivial, but for ZBlk1 it may seem that we could avoid
changing ZBlk object itself and mark only pointed-to ZData object as
changed. However that would be not correct to do if we consider
invalidations.

Noticed while working on WCFS.

Add package-level documentation to

  - bigfile/file_zodb.py,
  - bigarray/array_zodb.py, and
  - lib/zodb.py

The most interesting read is file_zodb.py .

Slightly improve documenation for functions in a couple of places.

Improving documentation was long overdue and it is improved only slightly by this commit.

This continues c7c01ce4 (bigfile/zodb: ZODB.Connection can migrate
between threads on close/open and we have to care): Until now we were
retrieving zconn.transaction_manager on _ZBigFileH init, and further using
that transaction manager for every connection reopen. However that is
not correct because on every reopen connection can be given new
transaction manager.

We were not practically hitting the bug because until recently ZODB was,
by default, using the same ThreadTransactionManager manager instance as
Connection.transaction_manager for all connections, and not doing all
steps needed to keep _ZBigFileH.transaction_manager in sync to
Connection was forgiven - a particular transaction manager that was used
was TransactionManager instance implicitly associated with current
thread by global threading.Local transaction.manager . However starting
from ZODB 5.5.0 Connection code was changed to remember as
.transaction_manager the particular TransactionManager instance without
any threading.Local games:

    https://github.com/zopefoundation/ZODB/commit/b6ac40f153
    https://github.com/zopefoundation/ZODB/issues/208
    https://github.com/zopefoundation/ZODB/pull/226

Given that we were not syncing properly that broke wendelin.core tests, for
example:

    bigfile/tests/test_filezodb.py::test_bigfile_filezodb_vs_conn_migration Exception in thread Thread-1:
    Traceback (most recent call last):
      File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
        self.run()
      File "/usr/lib/python2.7/threading.py", line 754, in run
        self.__target(*self.__args, **self.__kwargs)
      File "/home/kirr/src/wendelin/wendelin.core/bigfile/tests/test_filezodb.py", line 401, in T11
        transaction.commit()    # should be nothing
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/_manager.py", line 252, in commit
        return self.manager.commit()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/_manager.py", line 131, in commit
        return self.get().commit()
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/_transaction.py", line 298, in commit
        self._synchronizers.map(lambda s: s.beforeCompletion(self))
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/weakset.py", line 61, in map
        f(elt)
      File "/home/kirr/src/wendelin/venv/z-dev/local/lib/python2.7/site-packages/transaction/_transaction.py", line 298, in <lambda>
        self._synchronizers.map(lambda s: s.beforeCompletion(self))
      File "/home/kirr/src/wendelin/wendelin.core/bigfile/file_zodb.py", line 671, in beforeCompletion
        assert txn is zconn.transaction_manager.get()
    AssertionError

What is happening here is that one thread used the connection and
ZBigFile/_ZBigFileH associated with it, then the connection was closed
and released to DB pool. Then the connection was reopened but by another
thread and thus with different TransactionManager instance and oops -
_ZBigFileH.transaction_manager is different because it is
TransactionManager instance that was used by the first thread.

Fix it by resyncing _ZBigFileH.transaction_manager on every
connection reopen. No new test as existing tests already cover the
problem when run with ZODB >= 5.5.0 .

Relicense to GPLv3+ with wide exception for all Free Software / Open Source projects + Business options.

Nexedi stack is licensed under Free Software licenses with various exceptions
that cover three business cases:

- Free Software
- Proprietary Software
- Rebranding

As long as one intends to develop Free Software based on Nexedi stack, no
license cost is involved. Developing proprietary software based on Nexedi stack
may require a proprietary exception license. Rebranding Nexedi stack is
prohibited unless rebranding license is acquired.

Through this licensing approach, Nexedi expects to encourage Free Software
development without restrictions and at the same time create a framework for
proprietary software to contribute to the long term sustainability of the
Nexedi stack.

Please see https://www.nexedi.com/licensing for details, rationale and options.

This reverts commit 9ae42085.

When working with big arrays and accessing / changing it not in tiny
bits ZBlk1 is much slower compared to ZBlk0. See details here

    https://www.nexedi.com/blog/NXD-Document.Blog.Wendelin.Core.Release.0.5.Performance.Tests

and in

    13c0c17c (bigfile/zodb: Format #1 which is optimized for small changes)

Until we can rely on database handling both cases automatically,
projects which care about changing arrays in small parts can manually
set WENDELIN_CORE_ZBLK_FMT=ZBlk1 or under ERP5/SlapOS use this setting:

    slapos@2558aadd

And let's have it performant in "big data" case by default.

/cc @yusei, @klaus, @Tyagov
/reviewed-on !5

13c0c17c (bigfile/zodb: Format #1 which is optimized for small changes)
used BTree to organize ZBlk1 block's chunks and for loadblkdata() added
"TODO we are missing to free internal BTree structures on data load".

#3 besides other
things showed that even when we deactivate ZData objects, we are still
keeping them as ghosts occupying memory and the same for IOBucket
objects.

This all happens because there is no proper way to deactivate whole
btree - including internal buckets objects. And since internal buckets
are not deactivated, they stay in picklecache and thus hold a reference
to ZData objects and ZData objects in turn, even if explicitly
deactivated, stay in memory.

We can fix this all via implementing whole-btree deactivation procedure.

To do so we need to iterate over all btree buckets recursively, but
unfortunately there is no BTree API to access/iterate btree's buckets.
We can however still get reference to first top-level buckets via
gc.get_referents(btree) and then scan buckets further without hacks.

gc.get_referents(btree) is a hack, but

- it works in O(1)  (we only get pointers from btree, not scanning all
  gcable objects and deducing them)
- it works reliable if we filter out non-interesting objects.

So in the end it works.

Before the patch loading more and more ZBlk1 data with objgraph
instrumentation was showing itself like

    #                                    Nobj        δ
    wendelin.bigfile.file_zodb.ZData     7168      +512
    BTrees.IOBTree.IOBucket               238       +17
    BTrees.IOBTree.IOBTree                 14        +1

and after this patch we now have

    BTrees.IOBTree.IOBTree                 14        +1

we cannot remove that "IOBTree + 1", since ZBlk1 is holding direct
reference on it (via .chunktab) and we have to keep ZBlk1 live with
._v_zfile and ._v_zblk set for invalidation to work. "+1 IOBtree" is
however small - 144 bytes per 2M (= 0.006%) so we can neglect that the
same way we neglect keeping ZBlk1 staying live for each block.

For ZBlk1 we already compare ZData content about whether it was changed
compared to data already stored to DB, and do not store it twice if data
is the same.

However ZBlk itself is always marked as changed, if corresponding memory
page was dirtied. This results in transactions like

Trans #33915309 tid=03b6944919befeee time=2016-04-17 22:01:06.034237 offset=140320105842
    status=' ' user='...' description='...'
  # ... other parts, but no ZData here
  data #2 oid=000000000026fc4c size=79 class=wendelin.bigfile.file_zodb.ZBlk1

where ZBlk1 is committed the same without necessity.

NOTE we cannot avoid committing ZBlk in all cases, because it is used to signal
    other DB clients that a ZBlk needs to be invalidated and this way associated
    fileh pages are invalidated too.

    This cannot work via ZData, because ZData don't have back-pointer to
    ZBlk1 or to corresponding zfile.

ZBlk* objects are intermediate ZODB object in between data stored in
ZODB and memory pages managed by virtmem. As such, after they do their
job to either load data from DB to memory, or store from memory to DB,
it is not needed to keep them alive with duplicate content thus only
wasting memory.

ZBlk0 cares about this detail via "deactivating" ._v_blkdata in
loadblkdata() and __getstate__() prologues.

ZBlk1 did the same for load path in loadblkdata() prologue, but for
.__getstate__() it was not directly possible, because for ZBlk1 the
state is IOBTree, not one non-persistent object, and thus it first needs
to be processed by ZODB together with its subobjects on its way to
storage and only then all they deactivated.

So 13c0c17c (bigfile/zodb: Format #1 which is optimized for small
changes) only put TODO for memory-page -> DB path about not wasting
memory this way.

But the problem is relatively easy to solve:

    - we can deactivate ZData objects (leaf objects in ZBlk1.chunktab
      btree) by hooking into ZData.__getstate__() prologue;

    - we also need to care to deactivate chunks right away, which
      setblkdata() loaded to compare .data and found them to be not
      changed

This way we do not waste memory keeping intermediate ZData objects alive
with the same content as memory page after commit.

/cc @Tyagov

ZBlk1.setblkdata() has logic to detect CHUNKSIZE change, and if so
recreate whole chunktab from scratch for simplicity. There was a thinko
however - len(chunk.data) == CHUNKSIZE is ok and actually very often
happens when data does not have zeroes.

Because of this off-by-1 comparison mistake, ZData objects were
constantly created and thrown out instead of being reused which led to
fast ZODB growth.

Fix it.

/reported-by @Tyagov

Our current workloads are mostly a lot of small data changes and this is what
ZBlk1 was created for. Yes it has larger overhead for accessing data, but we
already painted the way how to handle this in 13c0c17c (bigfile/zodb: Format #1
which is optimized for small changes) -> move data deduplication/management to
server side.

So be it ZBlk1 the default for now.

/cc @Tyagov, @klaus

Our current approach is that each file block is represented by 1 zodb
object, with block size being 2M. Even with trailing \0 trimming, which
halves the overhead on average, DB size grows very fast if we do a lot
of small appends or changes. So another format needs to be introduced
which has lower overhead for storing small changes:

In general, to represent BigFile as ZODB objects, each file block could
be represented separately either as

    1) one ZODB object, or          (ZBlk0 - this what we have already)
    2) group of ZODB objects        (ZBlk1 - this is what we introduce)

with top-level BTree directory #blk -> objects representing block.

For "1" we have

    - low-overhead access time (only 1 object loaded from DB), but
    - high-overhead in terms of ZODB size (with FileStorage / ZEO, every change
      to a block causes it to be written into DB in full again)

For "2" we have

    - low-overhead in terms of ZODB size (only part of a block is overwritten
      in DB on single change), but
    - high-overhead in terms of access time
      (several objects need to be loaded for 1 block)

In general it is not possible to have low-overhead for both i) access-time, and
ii) DB size, with approach where we do block objects representation /
management on *client* side.

On the other hand, if object management is moved to DB *server* side, it is
possible to deduplicate them there and this way have low-overhead for both
access-time and DB size with just client storing 1 object per file block. This
will be our future approach after we teach NEO about object deduplication.

~~~~

As shown above in the last paragraph it is not possible to perform
optimally on client side. Thus ZBlk1 should be only an intermediate
solution until we move data management to DB server side, with main
criteria for ZBlk1 to keep it simple.

In this patch a simple scheme is used, where every block is divided into
chunks organized via BTree. When a block part changes, only corresponding
chunk is updated. Chunk size is chosen to be 4K which creates ~ 512
fanout for 2M block.

DB size after tests is changed as follows:

        bigfile     bigarray

ZBlk0     24K       6200K
ZBlk1     36K         36K

( slight size increase for bigfile tests is because of btree structures
  overhead )

Time to run tests stays approximately the same.

/cc @Tyagov, @klaus

- current ZBlk becomes format 0
- write format can be selected via WENDELIN_CORE_ZBLK_FMT env var
- upon writing a block we always make sure we write it in current write
  format - so if a block was previously written in one format, it could
  be changed on the next write.
- tox is prepared to test all write formats (so far only ZBlk0 there).

The reason is - in the next patch we'll introduce another format for
blocks which is optimized for small changes.

If we aim to have several kinds of ZBlk, the functionality to invalidate
a block and bind it to zfile is common and thus should be shared.

If we introduce a base class, it also makes sense to document what
.loadblkdata() and .setblkdata() should do there - in one place.

- we have logic to init ._v_zfile and ._v_blk there

- the same for ._v_blkdata - logic to init it is there + it is better to
  set variables right from instance creation, not hoping "it will be set
  outside from master"

  NOTE ._v_blkdata = None means the block was not yet loaded and
  generally fits into logic how ZBlk operates and thus the change is ok.

A lot of times data in blocks come shorter than block size and the rest
of the memory page is zeros (because it was pre-filled zeros by OS when
page was allocated).

Do a simple heuristic and trim those trailing zeros and not store them
into DB.

With this change size of DB created by running bigfile and bigarray
tests changes as following:

            bigfile     bigarray

    old     145M         35M
    new      24K          6M

Trimming trailing zeros is currently done with str.rstrip('\0') which
creates a copy. When/if needed this could be optimized to work in-place.

- to keep things uniform with counterpart .loadblkdata()
- so that master do not mess with ZBlk internals and works only through
  interface - this way it will be possible to use several
  kinds of ZBlk.

All those functions move data between DB and ._v_blkdata and only master
then connects data to memory page. Make that fact explicit.

Again, leftover from 4174b84a (bigfile: BigFile backend to store data in
ZODB).

The comment was a leftover there from 4174b84a (bigfile: BigFile backend
to store data in ZODB).

It was already done from the beginning in 4174b84a (bigfile: BigFile
backend to store data in ZODB).

When there is a conflict (on any object, but on ZBlk in particular) ZODB
machinery calls its ._p_invalidate() twice:

  File ".../wendelin.core/bigfile/tests/test_filezodb.py", line 661, in test_bigfile_filezodb_vs_conflicts
    tm2.commit()    # this should raise ConflictError and stay at 11 state
  File ".../transaction/_manager.py", line 111, in commit
    return self.get().commit()
  File ".../transaction/_transaction.py", line 271, in commit
    self._commitResources()
  File ".../transaction/_transaction.py", line 414, in _commitResources
    self._cleanup(L)
  File ".../transaction/_transaction.py", line 426, in _cleanup
    rm.abort(self)
  File ".../ZODB/Connection.py", line 436, in abort
    self._abort()
  File ".../ZODB/Connection.py", line 479, in _abort
    self._cache.invalidate(oid)
  File ".../wendelin.core/bigfile/file_zodb.py", line 148, in _p_invalidate
    traceback.print_stack()

and

  File ".../wendelin.core/bigfile/tests/test_filezodb.py", line 661, in test_bigfile_filezodb_vs_conflicts
    tm2.commit()    # this should raise ConflictError and stay at 11 state
  File ".../transaction/_manager.py", line 111, in commit
    return self.get().commit()
  File ".../transaction/_transaction.py", line 271, in commit
    self._commitResources()
  File ".../transaction/_transaction.py", line 416, in _commitResources
    self._synchronizers.map(lambda s: s.afterCompletion(self))
  File ".../transaction/weakset.py", line 59, in map
    f(elt)
  File ".../transaction/_transaction.py", line 416, in <lambda>
    self._synchronizers.map(lambda s: s.afterCompletion(self))
  File ".../ZODB/Connection.py", line 831, in _storage_sync
    self._flush_invalidations()
  File ".../ZODB/Connection.py", line 539, in _flush_invalidations
    self._cache.invalidate(invalidated)
  File ".../wendelin.core/bigfile/file_zodb.py", line 148, in _p_invalidate
    traceback.print_stack()

i.e. first invalidation is done by commit cleanup:

    https://github.com/zopefoundation/transaction/blob/1.4.4/transaction/_transaction.py#L414
    https://github.com/zopefoundation/ZODB/blob/3.10/src/ZODB/Connection.py#L479

and then Connection.afterCompletion() flushes invalidation again:

    https://github.com/zopefoundation/transaction/blob/1.4.4/transaction/_transaction.py#L416
    https://github.com/zopefoundation/ZODB/blob/3.10/src/ZODB/Connection.py#L833
    https://github.com/zopefoundation/ZODB/blob/3.10/src/ZODB/Connection.py#L539

If there was no conflict - there will be no ConflictError raised and
thus no Transaction._cleanup() done in its ._commitResources() ->
invalidation called only once. But with ConflictError - it is twice.

Adjust ZBlk._p_invalidate() not to delve into real invalidation more
than once - else we will fail, as ZBlk._v_zfile becomes unbound after
invalidation done the first time.

LivePersistent can go to ghost state, because invalidation cannot be
ignored, i.e. they indicate the object has been changed externally.

This does not break our logic for ZBigFile and ZBigArray as
invalidations can happen only at transaction boundary, so during the
course of transaction those classes are guaranteed to stay uptodate and
thus not loose ._v_file and ._v_fileh (which is the reason they inherit
from LivePersistent).

it is ok to loose ._v_file and ._v_fileh at transaction boundary and
become ghost - those objects will be recreated upon going back uptodate
and will stay alive again during the whole transaction window.

We care only not to loose e.g. ._v_fileh inside transaction, because
loosing that data manager and thus data it manages inside transaction
can break synchronization logic and forget changed-through-mmap data.

If we do - ZBigFileH objects just don't get garbage collected, and
sooner or later this way it leaks enough filedescriptors so that main
zope loop breaks:

    Traceback (most recent call last):
      File ".../bin/runzope", line 194, in <module>
        sys.exit(Zope2.Startup.run.run())
      File ".../eggs/Zope2-2.13.22-py2.7.egg/Zope2/Startup/run.py", line 26, in run
        starter.run()
      File ".../eggs/Zope2-2.13.22-py2.7.egg/Zope2/Startup/__init__.py", line 105, in run
        Lifetime.loop()
      File ".../eggs/Zope2-2.13.22-py2.7.egg/Lifetime/__init__.py", line 43, in loop
        lifetime_loop()
      File ".../eggs/Zope2-2.13.22-py2.7.egg/Lifetime/__init__.py", line 53, in lifetime_loop
        asyncore.poll(timeout, map)
      File ".../parts/python2.7/lib/python2.7/asyncore.py", line 145, in poll
        r, w, e = select.select(r, w, e, timeout)
    ValueError: filedescriptor out of range in select()

    $ lsof -p <runzope-pid> |grep ramh | wc -l
    950

So continuing 64d1f40b (bigfile/zodb: Monkey-patch for ZODB.Connection
to support callback on .open()) let's change the implementation to use
WeakSet for callbacks list.

Yes, because weakref to bound methods release immediately, we give up
flexibility to subscribe to arbitrary callbacks. If it become an issue,
something like WeakMethod from py3 or recipes from the net how to do it
are there.

ZODB 3.10.4 was released almost 4 years ago, and contains significant
change how ghost objects coming from DB are initially setup.

Continuing theme from the previous patch, here is propagation of
invalidation messages from ZODB to BigFileH memory.

The use-case here is that e.g. one fileh mapping was created in one
connection, another in another, and after doing changes in second
connection and committing there, the first fileh has to invalidate
appropriate already-loaded pages, so its next transaction won't work
with stale data.

To do it, we hook into ZBlk._p_invalidate() and propagate the
invalidation message to ZBigFile which then notifies all
opened-through-it ZBigFileH to invalidate a page.

ZBlk -> ZBigFile lookup is done without storing backpointer in ZODB -
instead, every time ZBigFile touches ZBlk object (and thus potentially
does GHOST -> Live transition to it), we (re-)bind it back to ZBigFile.
Since ZBigFile is the only class that works with ZBlk objects it is safe
to do so.

For ZBigFile to notify "all-opened-through-it" ZBigFileH, a weakset is
introduced to track them.

Otherwise the real page invalidation work is done by virtmem (see
previous patch).

Intro
-----

ZODB maintains pool of opened-to-DB connections. For each request Zope
opens 1 connection and, after request handling is done, returns the
connection back to ZODB pool (via Connection.close()). The same
connection will be opened again for handling some future next request at
some future time. This next open can happen in different-from-first
request worker thread.

TransactionManager  (as accessed by transaction.{get,commit,abort,...})
is thread-local, that is e.g. transaction.get() returns different
transaction for threads T1 and T2.

When _ZBigFileH hooks into txn_manager to get a chance to run its
.beforeCompletion() when transaction.commit() is run, it hooks into
_current_ _thread_ transaction manager.

Without unhooking on connection close, and circumstances where
connection migrates to different thread this can lead to
dissynchronization between ZBigFileH managing fileh pages and Connection
with ZODB objects. And even to data corruption, e.g.

    T1              T2

    open
    zarray[0] = 11
    commit
    close

                    open                # opens connection as closed in T1
    open
                    zarray[0] = 21
    commit
                    abort

    close           close

Here zarray[0]=21 _will_ be committed by T1 as part of T1 transaction -
because when T1 does commit .beforeCompletion() for zarray is invoked,
sees there is dirty data and propagate changes to zodb objects in
connection for T2, joins connection for T2 into txn for T1, and then txn
for t1 when doing two-phase-commit stores modified objects to DB ->
oops.

----------------------------------------

To prevent such dissynchronization _ZBigFileH needs to be a DataManager
which works in sync with the connection it was initially created under -
on connection close, unregister from transaction_manager, and on
connection open, register to transaction manager in current, possibly
different, thread context. Then there won't be incorrect
beforeCompletion() notification and corruption.

This issue, besides possible data corruption, was probably also exposing
itself via following ways we've seen in production (everywhere
connection was migrated from T1 to T2):

1. Exception ZODB.POSException.ConnectionStateError:
        ConnectionStateError('Cannot close a connection joined to a transaction',)
        in <bound method Cleanup.__del__ of <App.ZApplication.Cleanup instance at 0x7f10f4bab050>> ignored

     T1          T2

                 modify zarray
                 commit/abort    # does not join zarray to T2.txn,
                                 # because .beforeCompletion() is
                                 # registered in T1.txn_manager

     commit                      # T1 invokes .beforeCompletion()
     ...                         # beforeCompletion() joins ZBigFileH and zarray._p_jar (=T2.conn) to T1.txn
     ...                         # commit is going on in progress
     ...
     ...         close           # T2 thinks request handling is done and
     ...                         # and closes connection. But T2.conn is
     ...                         # still joined to T1.txn

2. Traceback (most recent call last):
     File ".../wendelin/bigfile/file_zodb.py", line 121, in storeblk
       def storeblk(self, blk, buf):   return self.zself.storeblk(blk, buf)
     File ".../wendelin/bigfile/file_zodb.py", line 220, in storeblk
       zblk._v_blkdata = bytes(buf)    # FIXME does memcpy
     File ".../ZODB/Connection.py", line 857, in setstate
       raise ConnectionStateError(msg)
   ZODB.POSException.ConnectionStateError: Shouldn't load state for 0x1f23a5 when the connection is closed

   Similar to "1", but close in T2 happens sooner, so that when T1 does
   the commit and tries to store object to database, Connection refuses to
   do the store:

     T1          T2

                 modify zarray
                 commit/abort

     commit
     ...         close
     ...
     ...
     . obj.store()
     ...
     ...

3. Traceback (most recent call last):
     File ".../wendelin/bigfile/file_zodb.py", line 121, in storeblk
       def storeblk(self, blk, buf):   return self.zself.storeblk(blk, buf)
     File ".../wendelin/bigfile/file_zodb.py", line 221, in storeblk
       zblk._p_changed = True          # if zblk was already in DB: _p_state -> CHANGED
     File ".../ZODB/Connection.py", line 979, in register
       self._register(obj)
     File ".../ZODB/Connection.py", line 989, in _register
       self.transaction_manager.get().join(self)
     File ".../transaction/_transaction.py", line 220, in join
       Status.ACTIVE, Status.DOOMED, self.status))
   ValueError: expected txn status 'Active' or 'Doomed', but it's 'Committing'

  ( storeblk() does zblk._p_changed -> Connection.register(zblk) ->
    txn.join() but txn is already committing

    IOW storeblk() was invoked with txn.state being already 'Committing' )

    T1          T2

                modify obj      # this way T2.conn joins T2.txn
                modify zarray

    commit                      # T1 invokes .beforeCompletion()
    ...                         # beforeCompletion() joins only _ZBigFileH to T1.txn
    ...                         # (because T2.conn is already marked as joined)
    ...
    ...         commit/abort    # T2 does commit/abort - this touches only T2.conn, not ZBigFileH
    ...                         # in particular T2.conn is now reset to be not joined
    ...
    . tpc_begin                 # actual active commit phase of T1 was somehow delayed a bit
    . tpc_commit                # when changes from RAM propagate to ZODB objects associated
    .  storeblk                 # connection (= T2.conn !) is notified again,
    .   zblk = ...              # wants to join txn for it thinks its transaction_manager,
                                # which when called from under T1 returns *T1* transaction manager for
                                # which T1.txn is already in state='Committing'

4. Empty transaction committed to NEO

   ( different from doing just transaction.commit() without changing
     any data - a connection was joined to txn, but set of modified
     object turned out to be empty )

   This is probably a race in Connection._register when both T1 and T2
   go to it at the same time:

   https://github.com/zopefoundation/ZODB/blob/3.10/src/ZODB/Connection.py#L988

   def _register(self, obj=None):
        if self._needs_to_join:
            self.transaction_manager.get().join(self)
            self._needs_to_join = False

    T1                          T2

                                modify zarray
    commit
    ...
    .beforeCompletion           modify obj
    . if T2.conn.needs_join      if T2.conn.needs_join      # race here
    .   T2.conn.join(T1.txn)       T2.conn.join(T2.txn)     # as a result T2.conn joins both T1.txn and T2.txn
    .
    commit finishes             # T2.conn registered-for-commit object list is now empty

                                commit
                                 tpc_begin
                                  storage.tpc_begin
                                 tpc_commit
                                  # no object stored, because for-commit-list is empty

/cc @jm, @klaus, @Tyagov, @vpelletier

ZODB.Connection has support for calling callbacks on .close() but not on
.open() . We'll need to hook into both Connection open/close process in the
next patch (for _ZBigFileH to stay in sync with Connection state).

NOTE

on-open  callbacks are setup once and fire many times on every open,
on-close callbacks are setup once and fire only once on next close.

The reason for this is that on-close callbacks are useful for scheduling
current connection cleanup, after its processing is done. But on-open
callback is for future connection usage, which is generally not related
to current connection.

/cc @jm, @vpelletier

This adds transactionality and with e.g. NEO[1] allows to distribute
objects to nodes into cluster.

We hook into ZODB two-phase commit process as a separate data manager,
and synchronize changes to memory, to changes to object only at that
time.

Alternative would be to get notified on every page change, and mark
appropriate object as dirty right at that moment.

But I wanted to stay close to filesystem design (we don't get
notification for every file change from kernel) - that's why it is done
the first way.

[1] http://www.neoppod.org/