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ZODB Programming

Installing ZODB

ZODB is packaged using the standard distutils tools.

Requirements

You will need Python 2.3 or higher. Since the code is packaged using distutils, it is simply a matter of untarring or unzipping the release package, and then running python setup.py install.

You'll need a C compiler to build the packages, because there are various C extension modules. Binary installers are provided for Windows users.

Installing the Packages

Download the ZODB tarball containing all the packages for both ZODB and ZEO from http://www.zope.org/Products/ZODB3.3. See the :file:`README.txt` file in the top level of the release directory for details on building, testing, and installing.

You can find information about ZODB and the most current releases in the ZODB Wiki at http://www.zope.org/Wikis/ZODB.

How ZODB Works

The ZODB is conceptually simple. Python classes subclass a :class:`persistent.Persistent` class to become ZODB-aware. Instances of persistent objects are brought in from a permanent storage medium, such as a disk file, when the program needs them, and remain cached in RAM. The ZODB traps modifications to objects, so that when a statement such as obj.size = 1 is executed, the modified object is marked as "dirty." On request, any dirty objects are written out to permanent storage; this is called committing a transaction. Transactions can also be aborted or rolled back, which results in any changes being discarded, dirty objects reverting to their initial state before the transaction began.

The term "transaction" has a specific technical meaning in computer science. It's extremely important that the contents of a database don't get corrupted by software or hardware crashes, and most database software offers protection against such corruption by supporting four useful properties, Atomicity, Consistency, Isolation, and Durability. In computer science jargon these four terms are collectively dubbed the ACID properties, forming an acronym from their names.

The ZODB provides all of the ACID properties. Definitions of the ACID properties are:

Atomicity
means that any changes to data made during a transaction are all-or-nothing. Either all the changes are applied, or none of them are. If a program makes a bunch of modifications and then crashes, the database won't be partially modified, potentially leaving the data in an inconsistent state; instead all the changes will be forgotten. That's bad, but it's better than having a partially- applied modification put the database into an inconsistent state.
Consistency
means that each transaction executes a valid transformation of the database state. Some databases, but not ZODB, provide a variety of consistency checks in the database or language; for example, a relational database constraint columns to be of particular types and can enforce relations across tables. Viewed more generally, atomicity and isolation make it possible for applications to provide consistency.
Isolation
means that two programs or threads running in two different transactions cannot see each other's changes until they commit their transactions.
Durability
means that once a transaction has been committed, a subsequent crash will not cause any data to be lost or corrupted.

Opening a ZODB

There are 3 main interfaces supplied by the ZODB: :class:`Storage`, :class:`DB`, and :class:`Connection` classes. The :class:`DB` and :class:`Connection` interfaces both have single implementations, but there are several different classes that implement the :class:`Storage` interface.

  • :class:`Storage` classes are the lowest layer, and handle storing and retrieving objects from some form of long-term storage. A few different types of Storage have been written, such as :class:`FileStorage`, which uses regular disk files, and :class:`BDBFullStorage`, which uses Sleepycat Software's BerkeleyDB database. You could write a new Storage that stored objects in a relational database, for example, if that would better suit your application. Two example storages, :class:`DemoStorage` and :class:`MappingStorage`, are available to use as models if you want to write a new Storage.
  • The :class:`DB` class sits on top of a storage, and mediates the interaction between several connections. One :class:`DB` instance is created per process.
  • Finally, the :class:`Connection` class caches objects, and moves them into and out of object storage. A multi-threaded program should open a separate :class:`Connection` instance for each thread. Different threads can then modify objects and commit their modifications independently.

Preparing to use a ZODB requires 3 steps: you have to open the :class:`Storage`, then create a :class:`DB` instance that uses the :class:`Storage`, and then get a :class:`Connection` from the :class:`DB instance`. All this is only a few lines of code:

from ZODB import FileStorage, DB

storage = FileStorage.FileStorage('/tmp/test-filestorage.fs')
db = DB(storage)
conn = db.open()

Note that you can use a completely different data storage mechanism by changing the first line that opens a :class:`Storage`; the above example uses a :class:`FileStorage`. In section :ref:`zeo`, "How ZEO Works", you'll see how ZEO uses this flexibility to good effect.

Using a ZODB Configuration File

ZODB also supports configuration files written in the ZConfig format. A configuration file can be used to separate the configuration logic from the application logic. The storages classes and the :class:`DB` class support a variety of keyword arguments; all these options can be specified in a config file.

The configuration file is simple. The example in the previous section could use the following example:

<zodb>
  <filestorage>
  path /tmp/test-filestorage.fs
  </filestorage>
</zodb>

The :mod:`ZODB.config` module includes several functions for opening database and storages from configuration files.

import ZODB.config

db = ZODB.config.databaseFromURL('/tmp/test.conf')
conn = db.open()

The ZConfig documentation, included in the ZODB3 release, explains the format in detail. Each configuration file is described by a schema, by convention stored in a :file:`component.xml` file. ZODB, ZEO, zLOG, and zdaemon all have schemas.

Writing a Persistent Class

Making a Python class persistent is quite simple; it simply needs to subclass from the :class:`Persistent` class, as shown in this example:

from persistent import Persistent

class User(Persistent):
    pass

The :class:`Persistent` base class is a new-style class implemented in C.

For simplicity, in the examples the :class:`User` class will simply be used as a holder for a bunch of attributes. Normally the class would define various methods that add functionality, but that has no impact on the ZODB's treatment of the class.

The ZODB uses persistence by reachability; starting from a set of root objects, all the attributes of those objects are made persistent, whether they're simple Python data types or class instances. There's no method to explicitly store objects in a ZODB database; simply assign them as an attribute of an object, or store them in a mapping, that's already in the database. This chain of containment must eventually reach back to the root object of the database.

As an example, we'll create a simple database of users that allows retrieving a :class:`User` object given the user's ID. First, we retrieve the primary root object of the ZODB using the :meth:`root` method of the :class:`Connection` instance. The root object behaves like a Python dictionary, so you can just add a new key/value pair for your application's root object. We'll insert an :class:`OOBTree` object that will contain all the :class:`User` objects. (The :class:`BTree` module is also included as part of Zope.)

dbroot = conn.root()

# Ensure that a 'userdb' key is present
# in the root
if not dbroot.has_key('userdb'):
    from BTrees.OOBTree import OOBTree
    dbroot['userdb'] = OOBTree()

userdb = dbroot['userdb']

Inserting a new user is simple: create the :class:`User` object, fill it with data, insert it into the :class:`BTree` instance, and commit this transaction.

# Create new User instance
import transaction

newuser = User()

# Add whatever attributes you want to track
newuser.id = 'amk'
newuser.first_name = 'Andrew' ; newuser.last_name = 'Kuchling'
...

# Add object to the BTree, keyed on the ID
userdb[newuser.id] = newuser

# Commit the change
transaction.commit()

The :mod:`transaction` module defines a few top-level functions for working with transactions. :func:`commit` writes any modified objects to disk, making the changes permanent. :func:`abort` rolls back any changes that have been made, restoring the original state of the objects. If you're familiar with database transactional semantics, this is all what you'd expect. :func:`get` returns a :class:`Transaction` object that has additional methods like :meth:`note`, to add a note to the transaction metadata.

More precisely, the :mod:`transaction` module exposes an instance of the :class:`ThreadTransactionManager` transaction manager class as transaction.manager, and the :mod:`transaction` functions :func:`get` and :func:`begin` redirect to the same-named methods of transaction.manager. The :func:`commit` and :func:`abort` functions apply the methods of the same names to the :class:`Transaction` object returned by transaction.manager.get(). This is for convenience. It's also possible to create your own transaction manager instances, and to tell DB.open() to use your transaction manager instead.

Because the integration with Python is so complete, it's a lot like having transactional semantics for your program's variables, and you can experiment with transactions at the Python interpreter's prompt:

>>> newuser
<User instance at 81b1f40>
>>> newuser.first_name           # Print initial value
'Andrew'
>>> newuser.first_name = 'Bob'   # Change first name
>>> newuser.first_name           # Verify the change
'Bob'
>>> transaction.abort()          # Abort transaction
>>> newuser.first_name           # The value has changed back
'Andrew'

Rules for Writing Persistent Classes

Practically all persistent languages impose some restrictions on programming style, warning against constructs they can't handle or adding subtle semantic changes, and the ZODB is no exception. Happily, the ZODB's restrictions are fairly simple to understand, and in practice it isn't too painful to work around them.

The summary of rules is as follows:

  • If you modify a mutable object that's the value of an object's attribute, the ZODB can't catch that, and won't mark the object as dirty. The solution is to either set the dirty bit yourself when you modify mutable objects, or use a wrapper for Python's lists and dictionaries (:class:`PersistentList`, :class:`PersistentMapping`) that will set the dirty bit properly.
  • Recent versions of the ZODB allow writing a class with :meth:`__setattr__` , :meth:`__getattr__`, or :meth:`__delattr__` methods. (Older versions didn't support this at all.) If you write such a :meth:`__setattr__` or :meth:`__delattr__` method, its code has to set the dirty bit manually.
  • A persistent class should not have a :meth:`__del__` method. The database moves objects freely between memory and storage. If an object has not been used in a while, it may be released and its contents loaded from storage the next time it is used. Since the Python interpreter is unaware of persistence, it would call :meth:`__del__` each time the object was freed.

Let's look at each of these rules in detail.

Modifying Mutable Objects

The ZODB uses various Python hooks to catch attribute accesses, and can trap most of the ways of modifying an object, but not all of them. If you modify a :class:`User` object by assigning to one of its attributes, as in userobj.first_name = 'Andrew', the ZODB will mark the object as having been changed, and it'll be written out on the following :meth:`commit`.

The most common idiom that isn't caught by the ZODB is mutating a list or dictionary. If :class:`User` objects have a attribute named friends containing a list, calling userobj.friends.append(otherUser) doesn't mark userobj as modified; from the ZODB's point of view, userobj.friends was only read, and its value, which happened to be an ordinary Python list, was returned. The ZODB isn't aware that the object returned was subsequently modified.

This is one of the few quirks you'll have to remember when using the ZODB; if you modify a mutable attribute of an object in place, you have to manually mark the object as having been modified by setting its dirty bit to true. This is done by setting the :attr:`_p_changed` attribute of the object to true:

userobj.friends.append(otherUser)
userobj._p_changed = True

You can hide the implementation detail of having to mark objects as dirty by designing your class's API to not use direct attribute access; instead, you can use the Java-style approach of accessor methods for everything, and then set the dirty bit within the accessor method. For example, you might forbid accessing the friends attribute directly, and add a :meth:`get_friend_list` accessor and an :meth:`add_friend` modifier method to the class. :meth:`add_friend` would then look like this:

def add_friend(self, friend):
    self.friends.append(otherUser)
    self._p_changed = True

Alternatively, you could use a ZODB-aware list or mapping type that handles the dirty bit for you. The ZODB comes with a :class:`PersistentMapping` class, and I've contributed a :class:`PersistentList` class that's included in my ZODB distribution, and may make it into a future upstream release of Zope.

:meth:`__getattr__`, :meth:`__delattr__`, and :meth:`__setattr__`

ZODB allows persistent classes to have hook methods like :meth:`__getattr__` and :meth:`__setattr__`. There are four special methods that control attribute access; the rules for each are a little different.

The :meth:`__getattr__` method works pretty much the same for persistent classes as it does for other classes. No special handling is needed. If an object is a ghost, then it will be activated before :meth:`__getattr__` is called.

The other methods are more delicate. They will override the hooks provided by :class:`Persistent`, so user code must call special methods to invoke those hooks anyway.

The :meth:`__getattribute__` method will be called for all attribute access; it overrides the attribute access support inherited from :class:`Persistent`. A user-defined :meth:`__getattribute__` must always give the :class:`Persistent` base class a chance to handle special attribute, as well as :attr:`__dict__` or :attr:`__class__`. The user code should call :meth:`_p_getattr`, passing the name of the attribute as the only argument. If it returns True, the user code should call :class:`Persistent`'s :meth:`__getattribute__` to get the value. If not, the custom user code can run.

A :meth:`__setattr__` hook will also override the :class:`Persistent` :meth:`__setattr__` hook. User code must treat it much like :meth:`__getattribute__`. The user-defined code must call :meth:`_p_setattr` first to all :class:`Persistent` to handle special attributes; :meth:`_p_setattr` takes the attribute name and value. If it returns True, :class:`Persistent` handled the attribute. If not, the user code can run. If the user code modifies the object's state, it must assigned to :attr:`_p_changed`.

A :meth:`__delattr__` hooks must be implemented the same was as a the last two hooks. The user code must call :meth:`_p_delattr`, passing the name of the attribute as an argument. If the call returns True, :class:`Persistent` handled the attribute; if not, the user code can run.

:meth:`__del__` methods

A :meth:`__del__` method is invoked just before the memory occupied by an unreferenced Python object is freed. Because ZODB may materialize, and dematerialize, a given persistent object in memory any number of times, there isn't a meaningful relationship between when a persistent object's :meth:`__del__` method gets invoked and any natural aspect of a persistent object's life cycle. For example, it is emphatically not the case that a persistent object's :meth:`__del__` method gets invoked only when the object is no longer referenced by other objects in the database. :meth:`__del__` is only concerned with reachability from objects in memory.

Worse, a :meth:`__del__` method can interfere with the persistence machinery's goals. For example, some number of persistent objects reside in a :class:`Connection`'s memory cache. At various times, to reduce memory burden, objects that haven't been referenced recently are removed from the cache. If a persistent object with a :meth:`__del___` method is so removed, and the cache was holding the last memory reference to the object, the object's :meth:`__del__` method will be invoked. If the :meth:`__del__` method then references any attribute of the object, ZODB needs to load the object from the database again, in order to satisfy the attribute reference. This puts the object back into the cache again: such an object is effectively immortal, occupying space in the memory cache forever, as every attempt to remove it from cache puts it back into the cache. In ZODB versions prior to 3.2.2, this could even cause the cache reduction code to fall into an infinite loop. The infinite loop no longer occurs, but such objects continue to live in the memory cache forever.

Because :meth:`__del__` methods don't make good sense for persistent objects, and can create problems, persistent classes should not define :meth:`__del__` methods.

Writing Persistent Classes

Now that we've looked at the basics of programming using the ZODB, we'll turn to some more subtle tasks that are likely to come up for anyone using the ZODB in a production system.

Changing Instance Attributes

Ideally, before making a class persistent you would get its interface right the first time, so that no attributes would ever need to be added, removed, or have their interpretation change over time. It's a worthy goal, but also an impractical one unless you're gifted with perfect knowledge of the future. Such unnatural foresight can't be required of any person, so you therefore have to be prepared to handle such structural changes gracefully. In object-oriented database terminology, this is a schema update. The ZODB doesn't have an actual schema specification, but you're changing the software's expectations of the data contained by an object, so you're implicitly changing the schema.

One way to handle such a change is to write a one-time conversion program that will loop over every single object in the database and update them to match the 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 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 function that would walk over every single object in a ZODB, checking each one to see if it's an instance of :class:`User`.

Some OODBs support a feature called extents, which allow quickly finding all the instances of a given class, no matter where they are in the object graph; unfortunately the ZODB doesn't offer extents as a feature.

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