Zope Object Database: object database and persistence

## Project description

The Zope Object Database provides an object-oriented database for Python that provides a high-degree of transparency. Applications can take advantage of object database features with few, if any, changes to application logic. ZODB includes features such as a plugable storage interface, rich transaction support, and undo.

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## ZODB

### Introduction

The ZODB package provides a set of tools for using the Zope Object Database (ZODB). The components you get with the ZODB release are as follows:

• Core ZODB, including the persistence machinery

• Standard storages such as FileStorage

• The persistent BTrees modules

• ZEO, for scalability needs

• documentation (needs more work)

Our primary development platforms are Linux, Mac OS X, and Windows XP. The test suite should pass without error on all of these platforms, although it can take a long time on Windows – longer if you use ZoneAlarm. Many particularly slow tests are skipped unless you pass –all as an argument to test.py.

### Compatibility

ZODB 3.9 requires Python 2.4.2 or later.

ZODB ZEO clients from ZODB 3.2 on can talk to ZODB 3.9 servers. ZODB ZEO Clients can talk to ZODB 3.8 and 3.9 ZEO servers.

### Prerequisites

You must have Python installed. If you’ve installed Python from RPM, be sure that you’ve installed the development RPMs too, since ZODB builds Python extensions. If you have the source release of ZODB, you will need a C compiler.

You also need the transaction, zc.lockfile, ZConfig, zdaemon, zope.event, zope.interface, zope.proxy and zope.testing packages. If you are using easy_install or zc.buildout to install ZODB, then these will be installed for you automatically.

### Installation

ZODB is released as a distutils package. The easiest ways to build and install it are to use easy_install, or zc.buildout.

To install by hand, first install the dependencies, ZConfig, zdaemon, zope.interface, zope.proxy and zope.testing. These can be found in the Python Package Index.

To build it, run the setup script:

% python setup.py build

The 64-bit support for the BTrees package may be enabled by using this build command instead:

% python setup.py build_ext -DZODB_64BIT_INTS build

To test the build, run the test script:

% python test.py

For more verbose test output, append one or two ‘-v’ arguments to this command.

If all the tests succeeded, you can install ZODB using the setup script:

% python setup.py install

This should now make all of ZODB accessible to your Python programs.

### Testing for Developers

The ZODB checkouts are buildouts. When working from a ZODB checkout, first run the bootstrap.py script to initialize the buildout:

% python bootstrap.py

and then use the buildout script to build ZODB and gather the dependencies:

% bin/buildout

This creates a test script:

% bin/test -v

This command will run all the tests, printing a single dot for each test. When it finishes, it will print a test summary. The exact number of tests can vary depending on platform and available third-party libraries.:

Ran 1182 tests in 241.269s

OK

The test script has many more options. Use the -h or --help options to see a file list of options. The default test suite omits several tests that depend on third-party software or that take a long time to run. To run all the available tests use the --all option. Running all the tests takes much longer.:

Ran 1561 tests in 1461.557s

OK

#### Maintenance scripts

Several scripts are provided with the ZODB and can help for analyzing, debugging, checking for consistency, summarizing content, reporting space used by objects, doing backups, artificial load testing, etc. Look at the ZODB/script directory for more informations.

### History

The historical version numbering schemes for ZODB and ZEO are complicated. Starting with ZODB 3.4, the ZODB and ZEO version numbers are the same.

In the ZODB 3.1 through 3.3 lines, the ZEO version number was “one smaller” than the ZODB version number; e.g., ZODB 3.2.7 included ZEO 2.2.7. ZODB and ZEO were distinct releases prior to ZODB 3.1, and had independent version numbers.

Historically, ZODB was distributed as a part of the Zope application server. Jim Fulton’s paper at the Python conference in 2000 described a version of ZODB he called ZODB 3, based on an earlier persistent object system called BoboPOS. The earliest versions of ZODB 3 were released with Zope 2.0.

Andrew Kuchling extracted ZODB from Zope 2.4.1 and packaged it for use by standalone Python programs. He called this version “StandaloneZODB”. Andrew’s guide to using ZODB is included in the Doc directory. This version of ZODB was hosted at http://sf.net/projects/zodb. It supported Python 1.5.2, and might still be of interest to users of this very old Python version.

Zope Corporation released a version of ZODB called “StandaloneZODB 1.0” in Feb. 2002. This release was based on Andrew’s packaging, but built from the same CVS repository as Zope. It is roughly equivalent to the ZODB in Zope 2.5.

Why not call the current release StandaloneZODB? The name StandaloneZODB is a bit of a mouthful. The standalone part of the name suggests that the Zope version is the real version and that this is an afterthought, which isn’t the case. So we’re calling this release “ZODB”. We also worked on a ZODB4 package for a while and made a couple of alpha releases. We’ve now abandoned that effort, because we didn’t have the resources to pursue ot while also maintaining ZODB(3).

The ZODB/ZEO Programming Guide included in the documentation is a modified version of Andrew Kuchling’s original guide, provided under the terms of the GNU Free Documentation License.

We maintain a Wiki page about all things ZODB, including status on future directions for ZODB. Please see

http://wiki.zope.org/ZODB/FrontPage

and feel free to contribute your comments. There is a Mailman mailing list in place to discuss all issues related to ZODB. You can send questions to

zodb-dev@zope.org

or subscribe at

http://lists.zope.org/mailman/listinfo/zodb-dev

and view its archives at

http://lists.zope.org/pipermail/zodb-dev

Note that Zope Corp mailing lists have a subscriber-only posting policy.

Andrew’s ZODB Programmers Guide is made available in several forms, including DVI and HTML. To view it online, point your browser at the file Doc/guide/zodb/index.html

## Change History

### 3.9.0b5 (2009-08-06)

Bugs Fixed

• Fixed vulnerabilities in the ZEO network protocol that allow:

• CVE-2009-0668 Arbitrary Python code execution in ZODB ZEO storage servers

• CVE-2009-0669 Authentication bypass in ZODB ZEO storage servers

The vulnerabilities only apply if you are using ZEO to share a database among multiple applications or application instances and if untrusted clients are able to connect to your ZEO servers.

### 3.9.0b3 (2009-07-30)

#### Bugs Fixed

• Simplified the setup script in hopes of working with bdist_rpm.

• Fixed the setup test command. It previously depended on private functions in zope.testing.testrunner that don’t exist any more.

• ZEO client threads were unnamed, making it hard to debug thread management.

• ZEO protocol 2 support was broken. This caused very old clients to be unable to use new servers.

• zeopack was less flexible than it was before. -h should default to local host.

• The “lawn” layout was being selected by default if the root of the blob directory happened to contain a hidden file or directory such as “.svn”. Now hidden files and directories are ignored when choosing the default layout.

• BlobStorage was not compatible with MVCC storages because the wrappers were being removed by each database connection. Fixed.

• Warn rather than fail if DB.open is called with an empty version string.

### 3.9.0b2 (2009-06-11)

Bugs Fixed

• Saving indexes for large file storages failed (with the error: RuntimeError: maximum recursion depth exceeded). This can cause a FileStorage to fail to start because it gets an error trying to save its index.

• Sizes of new objects weren’t added to the object cache size estimation, causing the object-cache size limiting feature to let the cache grow too large when many objects were added.

• Deleted records weren’t removed when packing file storages.

• Fixed intermittent failures in the MVCCMappingStorage tests.

• Fixed analyze.py and added test.

• ZEO client blob cache size management is a little bit more robust.

### 3.9.0b1 (2009-05-04)

#### New Features (in more or less reverse chronological order)

• The Database class now has an xrefs keyword argument and a corresponding allow-implicit-cross-references configuration option. which default to true. When set to false, cross-database references are disallowed.

• As a convenience, the connection root method for returning the root object can now also be used as an object with attributes mapped to the root-object keys.

• Databases have a new method, transaction, that can be used with the Python (2.5 and later) with statement:

db = ZODB.DB(...)
with db.transaction() as conn:
# ... do stuff with conn

This uses a private transaction manager for the connection. If control exists the block without an error, the transaction is committed, otherwise, it is aborted.

• Convenience functions ZODB.connection and ZEO.connection provide a convenient way to open a connection to a database. They open a database and return a connection to it. When the connection is closed, the database is closed as well.

• The ZODB.config databaseFrom… methods now support multi-databases. If multiple zodb sections are used to define multiple databases, the databases are connected in a multi-database arrangement and the first of the defined databases is returned.

• The zeopack script has gotten a number of improvements:

• Simplified command-line interface. (The old interface is still supported, except that support for ZEO version 1 servers has been dropped.)

• Multiple storages can be packed in sequence.

• This simplifies pack scheduling on servers serving multiple databases.

• All storages are packed to the same time.

• You can now specify a time of day to pack to.

• The script will now time out if it can’t connect to s storage in 60 seconds.

• The connection now estimates the object size based on its pickle size and informs the cache about size changes.

The database got additional configurations options (cache-size-bytes and historical-cache-size-bytes) to limit the cache size based on the estimated total size of cached objects. The default values are 0 which has the interpretation “do not limit based on the total estimated size”. There are corresponding methods to read and set the new configuration parameters.

• Connections now have a public opened attribute that is true when the connection is open, and false otherwise. When true, it is the seconds since the epoch (time.time()) when the connection was opened. This is a renaming of the previous _opened private variable.

• FileStorage now supports blobs directly.

• You can now control whether FileStorages keep .old files when packing.

• POSKeyErrors are no longer logged by ZEO servers, because they are really client errors.

• A new storage interface, IExternalGC, to support external garbage collection, http://wiki.zope.org/ZODB/ExternalGC, has been defined and implemented for FileStorage and ClientStorage.

• As a small convenience (mainly for tests), you can now specify initial data as a string argument to the Blob constructor.

• ZEO Servers now provide an option, invalidation-age, that allows quick verification of ZEO clients less than a given age even if the number of transactions the client hasn’t seen exceeds the invalidation queue size. This is only recommended if the storage being served supports effecient iteration from a point near the end of the transaction history.

• The FileStorage iterator now handles large files better. When iteratng from a starting transaction near the end of the file, the iterator will scan backward from the end of the file to find the starting point. This enhancement makes it practical to take advantage of the new storage server invalidation-age option.

• Previously, database connections were managed as a stack. This tended to cause the same connection(s) to be used over and over. For example, the most used conection would typically be the onlyt connection used. In some rare situations, extra connections could be opened and end up on the top of the stack, causing extreme memory wastage. Now, when connections are placed on the stack, they sink below existing connections that have more active objects.

• There is a new pool-timeout database configuration option to specify that connections unused after the given time interval should be garbage colection. This will provide a means of dealing with extra connections that are created in rare circumstances and that would consume an unreasonable amount of memory.

• The Blob open method now supports a new mode, ‘c’, to open committed data for reading as an ordinary file, rather than as a blob file. The ordinary file may be used outside the current transaction and even after the blob’s database connection has been closed.

• ClientStorage now provides blob cache management. When using non-shared blob directories, you can set a target cache size and the cache will periodically be reduced try to keep it below the target size.

The client blob directory layout has changed. If you have existing non-shared blob directories, you will have to remove them.

• ZODB 3.9 ZEO clients can connect to ZODB 3.8 servers. ZODB ZEO clients from ZODB 3.2 on can connect to ZODB 3.9 servers.

• When a ZEO cache is stale and would need verification, a ZEO.interfaces.StaleCache event is published (to zope.event). Applications may handle this event and take action such as exiting the application without verifying the cache or starting cold.

• There’s a new convenience function, ZEO.DB, for creating databases using ZEO Client Storages. Just call ZEO.DB with the same arguments you would otherwise pass to ZEO.ClientStorage.ClientStorage:

import ZEO
db = ZEO.DB(('some_host', 8200))
• Object saves are a little faster

• When configuring storages in a storage server, the storage name now defaults to “1”. In the overwhelmingly common case that a single storage, the name can now be ommitted.

• FileStorage now provides optional garbage collection. A ‘gc’ keyword option can be passed to the pack method. A false value prevents garbage collection.

• The FileStorage constructor now provides a boolean pack_gc option, which defaults to True, to control whether garbage collection is performed when packing by default. This can be overridden with the gc option to the pack method.

The ZConfig configuration for FileStorage now includes a pack-gc option, corresponding to the pack_gc constructor argument.

• The FileStorage constructor now has a packer keyword argument that allows an alternative packer to be supplied.

The ZConfig configuration for FileStorage now includes a packer option, corresponding to the packer constructor argument.

• MappingStorage now supports multi-version concurrency control and iteration and provides a better storage implementation example.

• DemoStorage has a number of new features:

• The ability to use a separate storage, such as a file storage to store changes

• Blob support

• Multi-version concurrency control and iteration

• Explicit support dfor demo-storage stacking via push and pop methods.

• Wen calling ZODB.DB to create a database, you can now pass a file name, rather than a storage to use a file storage.

• Added support for copying and recovery of blob storages:

• Added a helper function, ZODB.blob.is_blob_record for testing whether a data record is for a blob. This can be used when iterating over a storage to detect blob records so that blob data can be copied.

In the future, we may want to build this into a blob-aware iteration interface, so that records get blob file attributes automatically.

• Added the IBlobStorageRestoreable interfaces for blob storages that support recovery via a restoreBlob method.

• Updated ZODB.blob.BlobStorage to implement IBlobStorageRestoreable and to have a copyTransactionsFrom method that also copies blob data.

• New ClientStorage configuration option drop_cache_rather_verify. If this option is true then the ZEO client cache is dropped instead of the long (unoptimized) verification. For large caches, setting this option can avoid effective downtimes in the order of hours when the connection to the ZEO server was interrupted for a longer time.

• Cleaned-up the storage iteration API and provided an iterator implementation for ZEO.

• Versions are no-longer supported.

• Document conflict resolution (see ZODB/ConflictResolution.txt).

• Support multidatabase references in conflict resolution.

• Make it possible to examine oid and (in some situations) database name of persistent object references during conflict resolution.

• Moved the ‘transaction’ module out of ZODB. ZODB depends upon this module, but it must be installed separately.

• ZODB installation now requires setuptools.

• Added offset information to output of fstail script. Added test harness for this script.

• Added support for read-only, historical connections based on datetimes or serials (TIDs). See src/ZODB/historical_connections.txt.

• Now depend on zc.lockfile

#### Bugs Fixed

• fixed Python 2.6 compatibility issue with ZEO/zeoserverlog.py

• using hashlib.sha1 if available in order to avoid DeprecationWarning under Python 2.6

• The monitor server didn’t correctly report the actual number of clients.

• Packing could return spurious errors due to errors notifying disconnected clients of new database size statistics.

• Undo sometimes failed for FileStorages configured to support blobs.

• Starting ClientStorages sometimes failed with non-new but empty cache files.

• The history method on ZEO clients failed.

• Fix for bug #251037: Make packing of blob storages non-blocking.

• Fix for bug #220856: Completed implementation of ZEO authentication.

• Fix for bug #184057: Make initialisation of small ZEO client file cache sizes not fail.

• Fix for bug #184054: MappingStorage used to raise a KeyError during load instead of a POSKeyError.

• Fix for bug #181712: Make ClientStorage update lastTransaction directly after connecting to a server, even when no cache verification is necessary.

• Fixed bug in blob filesystem helper: the isSecure check was inversed.

• Fixed bug in transaction buffer: a tuple was unpacked incorrectly in clear.

• Bugfix the situation in which comparing persistent objects (for instance, as members in BTree set or keys of BTree) might cause data inconsistency during conflict resolution.

• Fixed bug 153316: persistent and BTrees were using int for memory sizes which caused errors on x86_64 Intel Xeon machines (using 64-bit Linux).

• Fixed small bug that the Connection.isReadOnly method didn’t work after a savepoint.

• Bug #98275: Made ZEO cache more tolerant when invalidating current versions of objects.

• Fixed a serious bug that could cause client I/O to stop (hang). This was accomonied by a critical log message along the lines of: “RuntimeError: dictionary changed size during iteration”.

• Fixed bug #127182: Blobs were subclassable which was not desired.

• Fixed bug #126007: tpc_abort had untested code path that was broken.

• Fixed bug #129921: getSize() function in BlobStorage could not deal with garbage files

• Fixed bug in which MVCC would not work for blobs.

• Fixed bug in ClientCache that occurred with objects larger than the total cache size.

• When an error occured attempting to lock a file and logging of said error was enabled.

• FileStorages previously saved indexes after a certain number of writes. This was done during the last phase of two-phase commit, which made this critical phase more subject to errors than it should have been. Also, for large databases, saves were done so infrequently as to be useless. The feature was removed to reduce the chance for errors during the last phase of two-phase commit.

• File storages previously kept an internal object id to transaction id mapping as an optimization. This mapping caused excessive memory usage and failures during the last phase of two-phase commit. This optimization has been removed.

• Refactored handling of invalidations on ZEO clients to fix a possible ordering problem for invalidation messages.

• On many systems, it was impossible to create more than 32K blobs. Added a new blob-directory layout to work around this limitation.

• Fixed bug that could lead to memory errors due to the use of a Python dictionary for a mapping that can grow large.

• Fixed bug #251037: Made packing of blob storages non-blocking.

• Fixed a bug that could cause InvalidObjectReference errors for objects that were explicitly added to a database if the object was modified after a savepoint that added the object.

• Fixed several bugs that caused ZEO cache corruption when connecting to servers. These bugs affected both persistent and non-persistent caches.

• Improved the the ZEO client shutdown support to try to avoid spurious errors on exit, especially for scripts, such as zeopack.

• Packing failed for databases containing cross-database references.

• Cross-database references to databases with empty names weren’t constructed properly.

• The zeo client cache used an excessive amount of memory, causing applications with large caches to exhaust available memory.

• Fixed a number of bugs in the handling of persistent ZEO caches:

• Cache records are written in several steps. If a process exits after writing begins and before it is finishes, the cache will be corrupt on restart. The way records are writted was changed to make cache record updates atomic.

• There was no lock file to prevent opening a cache multiple times at once, which would lead to corruption. Persistent caches now use lock files, in the same way that file storages do.

• A bug in the cache-opening logic led to cache failure in the unlikely event that a cache has no free blocks.

• When using ZEO Client Storages, Errors occured when trying to store objects too big to fit in the ZEO cache file.

• Fixed bug in blob filesystem helper: the isSecure check was inversed.

• Fixed bug in transaction buffer: a tuple was unpacked incorrectly in clear.

• Fixed bug #190884: Wrong reference to POSKeyError caused NameError.

• Completed implementation of ZEO authentication. This fixes issue 220856.

## Project details

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