Merge pull request #105 from zopefoundation/transactions-and-threading

Documentation on transactions and threading.

CHANGES.rst

@@ -17,6 +17,8 @@
   ``transaction_manager`` was the (default) thread-local manager. See
   `issue 114 <https://github.com/zopefoundation/ZODB/issues/114>`_.
 
+- Many docstrings have been improved.
+
 5.0.0 (2016-09-06)
 ==================
 

doc/articles/old-guide/prog-zodb.rst

@@ -435,7 +435,7 @@ new schema.  This can be easy if your network of object references is quite
 structured, making it easy to find all the instances of the class being
 modified.  For example, if all :class:`User` objects can be found inside a
 single dictionary or BTree, then it would be a simple matter to loop over every
-:class:`User` instance with a :keyword:`for` statement. This is more difficult
+:class:`User` instance with a ``for`` statement. This is more difficult
 if your object graph is less structured; if :class:`User` objects can be found
 as attributes of any number of different class instances, then there's no longer
 any easy way to find them all, short of writing a generalized object traversal

doc/guide/index.rst

@@ -14,13 +14,11 @@ If you haven't yet, you should read the :ref:`Tutorial <tutorial-label>`.
 
    install-and-run
    writing-persistent-objects.rst
+   transactions-and-threading
 
 .. todo:
 
-   transaction.rst
-   storages.rst
-   configuration.rst
-   threading.rst
-   packing-and-garbage-collection.rst
-   blobs.rst
-   multi-databases.rst
+   blobs
+   packing-and-garbage-collection
+   multi-databases
+   blobs

doc/guide/install-and-run.rst

@@ -128,6 +128,8 @@ much of anything.  Connections take care of loading and saving objects
 and manage object caches. Each connection has it's own cache
 [#caches-are-expensive]_.
 
+.. _getting-connections:
+
 Getting connections
 -------------------
 
@@ -144,7 +146,7 @@ db.open()
    done using the connection.
 
    If changes are made, the application :ref:`commits transactions
-   <commit-transactions>` to make them permanent.
+   <using-transactions-label>` to make them permanent.
 
 db.transaction()
    The database :meth:`~ZODB.DB.transaction` method

doc/guide/transactions-and-threading.rst

+============================
+Transactions and concurrency
+============================
+
+.. contents::
+
+`Transactions <https://en.wikipedia.org/wiki/Database_transaction>`_
+are a core feature of ZODB.  Much has been written about transactions,
+and we won't go into much detail here.  Transactions provide two core
+benefits:
+
+Atomicity
+  When a transaction executes, it succeeds or fails completely. If
+  some data are updated and then an error occurs, causing the
+  transaction to fail, the updates are rolled back automatically. The
+  application using the transactional system doesn't have to undo
+  partial changes.  This takes a significant burden from developers
+  and increases the reliability of applications.
+
+Concurrency
+  Transactions provide a way of managing concurrent updates to data.
+  Different programs operate on the data independently, without having
+  to use low-level techniques to moderate their access. Coordination
+  and synchronization happen via transactions.
+
+
+.. _using-transactions-label:
+
+Using transactions
+==================
+
+All activity in ZODB happens in the context of database connections
+and transactions.  Here's a simple example::
+
+  import ZODB, transaction
+  db = ZODB.DB(None) # Use a mapping storage
+  conn = db.open()
+
+  conn.root.x = 1
+  transaction.commit()
+
+.. -> src
+
+   >>> exec(src)
+
+In the example above, we used ``transaction.commit()`` to commit a
+transaction, making the change to ``conn.root`` permanent.  This is
+the most common way to use ZODB, at least historically.
+
+If we decide we don't want to commit a transaction, we can use
+``abort``::
+
+  conn.root.x = 2
+  transaction.abort() # conn.root.x goes back to 1
+
+.. -> src
+
+   >>> exec(src)
+   >>> conn.root.x
+   1
+   >>> conn.close()
+
+In this example, because we aborted the transaction, the value of
+``conn.root.x`` was rolled back to 1.
+
+There are a number of things going on here that deserve some
+explanation.  When using transactions, there are three kinds of
+objects involved:
+
+Transaction
+   Transactions represent units of work.  Each transaction has a beginning and
+   an end. Transactions provide the
+   :interface:`~transaction.interfaces.ITransaction` interface.
+
+Transaction manager
+   Transaction managers create transactions and
+   provide APIs to start and end transactions.  The transactions
+   managed are always sequential. There is always exactly one active
+   transaction associated with a transaction manager at any point in
+   time. Transaction managers provide the
+   :interface:`~transaction.interfaces.ITransactionManager` interface.
+
+Data manager
+   Data managers manage data associated with transactions.  ZODB
+   connections are data managers.  The details of how they interact
+   with transactions aren't important here.
+
+Explicit transaction managers
+-----------------------------
+
+ZODB connections have transaction managers associated with them when
+they're opened. When we call the database :meth:`~ZODB.DB.open` method
+without an argument, a thread-local transaction manager is used. Each
+thread has its own transaction manager.  When we called
+``transaction.commit()`` above we were calling commit on the
+thread-local transaction manager.
+
+Because we used a thread-local transaction manager, all of the work in
+the transaction needs to happen in the same thread.  Similarly, only
+one transaction can be active in a thread.
+
+If we want to run multiple simultaneous transactions in a single
+thread, or if we want to spread the work of a transaction over
+multiple threads [#bad-idea-using-multiple-threads-per-transaction]_,
+then we can create transaction managers ourselves and pass them to
+:meth:`~ZODB.DB.open`::
+
+  my_transaction_manager = transaction.TransactionManager()
+  conn = db.open(my_transaction_manager)
+  conn.root.x = 2
+  my_transaction_manager.commit()
+
+.. -> src
+
+   >>> exec(src)
+
+In this example, to commit our work, we called ``commit()`` on the
+transaction manager we created and passed to :meth:`~ZODB.DB.open`.
+
+Context managers
+----------------
+
+In the examples above, the transaction beginnings were
+implicit. Transactions were effectively
+[#implicit-transaction-creation]_ created when the transaction
+managers were created and when previous transactions were committed.
+We can create transactions explicitly using
+:meth:`~transaction.interfaces.ITransactionManager.begin`::
+
+  my_transaction_manager.begin()
+
+.. -> src
+
+   >>> exec(src)
+
+A more modern [#context-managers-are-new]_ way to manage transaction
+boundaries is to use context managers and the Python ``with``
+statement. Transaction managers are context managers, so we can use
+them with the ``with`` statement directly::
+
+  with my_transaction_manager as trans:
+     trans.note("incrementing x")
+     conn.root.x += 1
+
+.. -> src
+
+   >>> exec(src)
+   >>> conn.root.x
+   3
+
+
+When used as a context manager, a transaction manager explicitly
+begins a new transaction, executes the code block and commits the
+transaction if there isn't an error and aborts it of there is an
+error.
+
+We used ``as trans`` above to get the transaction.
+
+Databases provide the :meth:`~ZODB.DB.transaction` method to execute a code
+block as a transaction::
+
+  with db.transaction() as conn2:
+     conn2.root.x += 1
+
+.. -> src
+
+   >>> exec(src)
+
+This opens a connection, assignes it its own context manager, and
+executes the nested code in a transaction.  We used ``as conn2`` to
+get the connection.  The transaction boundaries are defined by the
+``with`` statement.
+
+Getting a connection's transaction manager
+------------------------------------------
+
+In the previous example, you may have wondered how one might get the
+current transaction. Every connection has an associated transaction
+manager, which is available as the ``transaction_manager`` attribute.
+So, for example, if we wanted to set a transaction note::
+
+
+  with db.transaction() as conn2:
+     conn2.transaction_manager.get().note("incrementing x again")
+     conn2.root.x += 1
+
+.. -> src
+
+   >>> exec(src)
+   >>> db.history(conn.root()._p_oid)[0]['description']
+   'incrementing x again'
+
+Here, we used the
+:meth:`~transaction.interfaces.ITransactionManager.get` method to get
+the current transaction.
+
+Connection isolation
+--------------------
+
+In the last few examples, we used a connection opened using
+:meth:`~ZODB.DB.transaction`.  This was distinct from and used a
+different transaction manager than the original connection. If we
+looked at the original connection, ``conn``, we'd see that it has the
+same value for ``x`` that we set earlier:
+
+  >>> conn.root.x
+  3
+
+This is because it's still in the same transaction that was begun when
+a change was last committed against it.  If we want to see changes, we
+have to begin a new transaction:
+
+  >>> trans = my_transaction_manager.begin()
+  >>> conn.root.x
+  5
+
+ZODB uses a timestamp-based commit protocol that provides `snapshot
+isolation <https://en.wikipedia.org/wiki/Snapshot_isolation>`_.
+Whenever we look at ZODB data, we see its state as of the time the
+transaction began.
+
+.. _conflicts-label:
+
+Conflict errors
+---------------
+
+As mentioned in the previous section, each connection sees and
+operates on a view of the database as of the transaction start time.
+If two connections modify the same object at the same time, one of the
+connections will get a conflict error when it tries to commit::
+
+  with db.transaction() as conn2:
+     conn2.root.x += 1
+
+  conn.root.x = 9
+  my_transaction_manager.commit() # will raise a conflict error
+
+.. -> src
+
+    >>> exec(src) # doctest: +ELLIPSIS
+    Traceback (most recent call last):
+    ...
+    ZODB.POSException.ConflictError: ...
+
+If we executed this code, we'd get ``ConflictError`` exception on the
+last line.  After a conflict error is raised, we'd need to abort the
+transaction, or begin a new one, at which point we'd see the data as
+written by the other connection:
+
+    >>> my_transaction_manager.abort()
+    >>> conn.root.x
+    6
+
+The timestamp-based approach used by ZODB is referred to as an
+*optimistic* approach, because it works best if there are no
+conflicts.
+
+The best way to avoid conflicts is to design your application so that
+multiple connections don't update the same object at the same time.
+This isn't always easy.
+
+Sometimes you may need to queue some operations that update shared
+data structures, like indexes, so the updates can be made by a
+dedicated thread or process, without making simultaneous updates.
+
+Retrying transactions
+~~~~~~~~~~~~~~~~~~~~~
+
+The most common way to deal with conflict errors is to catch them and
+retry transactions.  To do this manually, involves code that looks
+something like this::
+
+  max_attempts = 3
+  attempts = 0
+  while True:
+      try:
+          with transaction.manager:
+              ... code that updates a database
+      except transaction.interfaces.TransientError:
+          attempts += 1
+          if attempts == max_attempts:
+              raise
+      else:
+          break
+
+In the example above, we used ``transaction.manager`` to refer to the
+thread-local transaction manager, which we then used used with the
+``with`` statement.  When a conflict error occurs, the transaction
+must be aborted before retrying the update. Using the transaction
+manager as a context manager in the ``with`` statement takes care of this
+for us.
+
+The example above is rather tedious.  There are a number of tools to
+automate transaction retry.  The `transaction
+<http://zodb.readthedocs.io/en/latest/transactions.html#retrying-transactions>`_
+package provides a context-manager-based mechanism for retrying
+transactions::
+
+  for attempt in transaction.manager.attempts():
+      with attempt:
+          ... code that updates a database
+
+Which is shorter and simpler [#but-obscure]_.
+
+For Python web frameworks, there are WSGI [#wtf-wsgi]_ middle-ware
+components, such as `repoze.tm2
+<https://pypi.python.org/pypi/repoze.tm2>`_ that align transaction
+boundaries with HTTP requests and retry transactions when there are
+transient errors.
+
+For applications like queue workers or `cron jobs
+<https://en.wikipedia.org/wiki/Cron>`_, conflicts can sometimes be
+allowed to fail, letting other queue workers or subsequent cron-job
+runs retry the work.
+
+Conflict resolution
+~~~~~~~~~~~~~~~~~~~
+
+ZODB provides a conflict-resolution framework for merging conflicting
+changes.  When conflicts occur, conflict resolution is used, when
+possible, to resolve the conflicts without raising a ConflictError to
+the application.
+
+Commonly used objects that implement conflict resolution are
+buckets and ``Length`` objects provided by the `BTree
+<https://pythonhosted.org/BTrees/>`_ package.
+
+The main data structures provided by BTrees: BTrees and TreeSets,
+spread their data over multiple objects.  The leaf-level objects,
+called *buckets*, allow distinct keys to be updated without causing
+conflicts [#usually-avoids-conflicts]_.
+
+``Length`` objects are conflict-free counters, that merge changes by
+simply accumulating changes.
+
+.. caution::
+   Conflict resolution weakens consistency.  Resist the temptation to
+   try to implement conflict resolution yourself.  In the future, ZODB
+   will provide greater control over conflict resolution, including
+   the option of disabling it.
+
+   It's generally best to avoid conflicts in the first place, if possible.
+
+ZODB and atomicity
+==================
+
+ZODB provides atomic transactions. When using ZODB, it's important to
+align work with transactions.  Once a transaction is committed, it
+can't be rolled back [#undo]_ automatically.  For applications, this
+implies that work that should be atomic shouldn't be split over
+multiple transactions.  This may seem somewhat obvious, but the rule
+can be broken in non-obvious ways. For example a Web API that splits
+logical operations over multiple web requests, as is often done in
+`REST
+<https://en.wikipedia.org/wiki/Representational_state_transfer>`_
+APIs, violate this rule.
+
+Partial transaction error recovery using savepoints
+---------------------------------------------------
+
+A transaction can be split into multiple steps that can be rolled back
+individually.  This is done by creating savepoints.  Changes in a
+savepoint can be rolled back without rolling back an entire
+transaction::
+
+  import ZODB
+  db = ZODB.DB(None) # using a mapping storage
+  with db.transaction() as conn:
+      conn.root.x = 1
+      conn.root.y = 0
+      savepoint = conn.transaction_manager.savepoint()
+      conn.root.y = 2
+      savepoint.rollback()
+
+  with db.transaction() as conn:
+      print([conn.root.x, conn.root.y]) # prints 1 0
+
+.. -> src
+
+   >>> exec(src)
+   [1, 0]
+
+If we executed this code, it would print 1 and 0, because while the
+initial changes were committed, the changes in the savepoint were
+rolled back.
+
+A secondary benefit of savepoints is that they save any changes made
+before the savepoint to a file, so that memory of changed objects can
+be freed if they aren't used later in the transaction.
+
+Concurrency, threads and processes
+==================================
+
+ZODB supports concurrency through transactions.  Multiple programs
+[#wtf-program]_ can operate independently in separate transactions.
+They synchronize at transaction boundaries.
+
+The most common way to run ZODB is with each program running in it's
+own thread.  Usually the thread-local transaction manager is used.
+
+You can use multiple threads per transaction and you can run multiple
+transactions in a single thread. To do this, you need to instantiate
+and use your own transaction manager, as described in `Explicit
+transaction managers`_.  To run multiple transaction managers
+simultaneously in a thread, you need to use a separate transaction
+manager for each transaction.
+
+To spread a transaction over multiple threads, you need to keep in
+mind that database connections, transaction managers and transactions
+are **not thread-safe**.  You have to prevent simultaneous access from
+multiple threads.  For this reason, **using multiple threads with a
+single transaction is not recommended**, but it is possible with care.
+
+Using multiple processes
+------------------------
+
+Using multiple Python processes is a good way to scale an application
+horizontally, especially given Python's `global interpreter lock
+<https://wiki.python.org/moin/GlobalInterpreterLock>`_.
+
+Some things to keep in mind when utilizing multiple processes:
+
+- If using the :mod:`multiprocessing` module, you can't
+  [#cant-share-now]_ share databases or connections between
+  processes. When you launch a subprocess, you'll need to
+  re-instantiate your storage and database.
+
+- You'll need to use a storage such as `ZEO
+  <https://github.com/zopefoundation/ZEO>`_, `RelStorage
+  <http://relstorage.readthedocs.io/en/latest/>`_, or `NEO
+  <http://www.neoppod.org/>`_, that supports multiple processes.  None
+  of the included storages do.
+
+.. [#but-obscure] But also a bit obscure.  The Python context-manager
+   mechanism isn't a great fit for the transaction-retry use case.
+
+.. [#wtf-wsgi] `Web Server Gateway Interface
+   <http://wsgi.readthedocs.io/en/latest/>`_
+
+.. [#usually-avoids-conflicts] Conflicts can still occur when buckets
+   split due to added objects causing them to exceed their maximum size.
+
+.. [#undo] Transactions can't be rolled back, but they may be undone
+   in some cases, especially of subsequent transactions
+   haven't modified the same objects.
+
+.. [#bad-idea-using-multiple-threads-per-transaction] While it's
+   possible to spread transaction work over multiple threads, **it's
+   not a good idea**. See `Concurrency, threads and processes`_
+
+.. [#implicit-transaction-creation] Transactions are implicitly
+   created when needed, such as when data are first modified.
+
+.. [#context-managers-are-new] ZODB and the transaction package
+   predate context managers and the Python ``with`` statement.
+
+.. [#wtf-program] We're using *program* here in a fairly general
+   sense, meaning some logic that we want to run to
+   perform some function, as opposed to an operating system program.
+
+.. [#cant-share-now] at least not now.

doc/reference/index.rst

@@ -6,6 +6,6 @@ Reference Documentation
 .. toctree::
    :maxdepth: 2
 
-   zodb.rst
-   storages.rst
- 
+   zodb
+   storages
+   transaction

doc/reference/transaction.rst

+============
+Transactions
+============
+
+Transaction support is provided by the `transaction
+<http://transaction.readthedocs.io/en/latest/>`_ package
+[#transaction-package-can-be-used-wo-ZODB]_, which is installed
+automatically when you install ZODB.  There are two important APIs
+provided by the transaction package, ``ITransactionManager`` and
+``ITransaction``, described below.
+
+ITransactionManager
+===================
+
+.. autointerface:: transaction.interfaces.ITransactionManager
+   :members: begin, get, commit, abort, doom, isDoomed, savepoint
+
+ITransaction
+============
+
+.. autointerface:: transaction.interfaces.ITransaction
+   :members: user, description, commit, abort, doom, savepoint, note,
+             setUser, setExtendedInfo,
+             addBeforeCommitHook, getBeforeCommitHooks,
+             addAfterCommitHook, getAfterCommitHooks
+
+
+.. [#transaction-package-can-be-used-wo-ZODB] The :mod:transaction
+   package is a general purpose package for managing `distributed
+   transactions
+   <https://en.wikipedia.org/wiki/Distributed_transaction>`_ with a
+   `two-phase commit protocol
+   <https://en.wikipedia.org/wiki/Two-phase_commit_protocol>`_.  It
+   can and occasionally is used with packages other than ZODB.

doc/reference/zodb.rst

@@ -84,7 +84,8 @@ Connections
 .. autoclass:: ZODB.Connection.Connection
    :members: add, cacheGC, cacheMinimize, close, db, get,
              getDebugInfo, get_connection, isReadOnly, oldstate,
-             onCloseCallback, root, setDebugInfo, sync
+             onCloseCallback, root, setDebugInfo, sync,
+             transaction_manager
 
 TimeStamp (transaction ids)
 ===========================

src/ZODB/Connection.py

@@ -50,6 +50,8 @@ import six
 
 from .mvccadapter import HistoricalStorageAdapter
 
+from . import valuedoc
+
 global_reset_counter = 0
 
 noop = lambda : None
@@ -88,6 +90,9 @@ class Connection(ExportImport, object):
 
     _code_timestamp = 0
 
+    #: Transaction manager associated with the connection when it was opened.
+    transaction_manager = valuedoc.ValueDoc('current transaction manager')
+
     ##########################################################################
     # Connection methods, ZODB.IConnection
 

src/ZODB/tests/testdocumentation.py

@@ -40,9 +40,12 @@ def test_suite():
 
     return unittest.TestSuite((
         manuel.testing.TestSuite(
-            manuel.doctest.Manuel() + manuel.capture.Manuel(),
+            manuel.doctest.Manuel(
+                optionflags=doctest.IGNORE_EXCEPTION_DETAIL,
+                ) + manuel.capture.Manuel(),
             join(guide, 'writing-persistent-objects.rst'),
             join(guide, 'install-and-run.rst'),
+            join(guide, 'transactions-and-threading.rst'),
             join(reference, 'zodb.rst'),
             join(reference, 'storages.rst'),
             setUp=setUp, tearDown=tearDown,