This documentation relates to an old version of DSpace, version 5.x. Looking for another version? See all documentation.
In this section, we explain the storage layer: the database structure, maintenance, and the bistream store and configurations.
RDBMS / Database Structure
DSpace uses a relational database to store all information about the organization of content, metadata about the content, information about e-people and authorization, and the state of currently-running workflows. The DSpace system also uses the relational database in order to maintain indices that users can browse.
DSpace 5 database schema (Postgres). Click on the thumbnail, then right-click the image and choose "Save as" to save in full resolution. Instructions on updating this schema diagram are in How to update database schema diagram.
Most of the functionality that DSpace uses can be offered by any standard SQL database that supports transactions. However at this time, DSpace APIS use some features specific to PostgreSQL and Oracle, so some modification to the code would be needed before DSpace would function fully with an alternative database back-end.
org.dspace.storage.rdbms package provides access to an SQL database in a somewhat simpler form than using JDBC directly. The primary class is
DatabaseManager, which executes SQL queries and returns
The database schema used by DSpace is initialized and upgraded automatically using Flyway DB. The
DatabaseUtils class manages all Flyway API calls, and executes the SQL migrations under the
org.dspace.storage.rdbms.sqlmigration package and the Java migrations under the
org.dspace.storage.rdbms.migration package. While Flyway is automatically initialized and executed during the initialization of
DatabaseManager, various Database Utilities are also available on the command line.
New in DSpace 5.x: Metadata for all DSpace objects
There were several changes between the DSpace 4 and 5 database schema, related to the new "Metadata for all Dspace objects" improvements. Full detail can be found here:
Maintenance and Backup
When using PostgreSQL, it's a good idea to perform regular 'vacuuming' of the database to optimize performance. By default, PostgreSQL performs automatic vacuuming on your behalf. However, if you have this feature disabled, then we recommend scheduling the
vacuumdb command to run on a regular basis.
Backups: The DSpace database can be backed up and restored using usual PostgreSQL Backup and Restore methods, for example with
psql. However when restoring a database, you will need to perform these additional steps:
After restoring a backup, you will need to reset the primary key generation sequences so that they do not produce already-used primary keys. Do this by executing the SQL in
[dspace]/etc/postgres/update-sequences.sql, for example with:
Configuring the RDBMS Component
The database manager is configured with the following properties in
The JDBC URL to use for accessing the database. This should not point to a connection pool, since DSpace already implements a connection pool.
JDBC driver class name. Since presently, DSpace uses PostgreSQL-specific features, this should be org.postgresql.Driver.
Username to use when accessing the database.
Corresponding password ot use when accessing the database.
Custom RDBMS tables, colums or views
When at all possible, we recommend creating custom database tables or views within a separate schema from the DSpace database tables. Since the DSpace database is initialized and upgraded automatically using Flyway DB, the upgrade process may stumble or throw errors if you've directly modified the DSpace database schema, views or tables. Flyway itself assumes it has full control over the DSpace database schema, and it is not "smart" enough to know what to do when it encounters a locally customized database.
That being said, if you absolutely need to customize your database tables, columns or views, it is possible to create custom Flyway migration scripts, which should make your customizations easier to manage in future upgrades. (Keep in mind though, that you may still need to maintain/update your custom Flyway migration scripts if they ever conflict directly with future DSpace database changes. The only way to "future proof" your local database changes is to try and make them as independent as possible, and avoid directly modifying the DSpace database schema as much as possible.)
If you wish to add custom Flyway migrations, they may be added to the following locations:
- Custom Flyway SQL migrations may be added anywhere under the
- Custom Flyway Java migrations may be added anywhere under the
- Additionally, for backwards support, custom SQL migrations may also be placed in the
[dspace]/etc/postgres/for a PostgreSQL specific migration script)
Adding Flyway migrations to any of the above location will cause Flyway to auto-discover the migration. It will be run in the order in which it is named. Our DSpace Flyway script naming convention follows Flyway best practices and is as follows:
- SQL script names:
V5.0_2014.09.26__DS-1582_Metadata_For_All_Objects.sqlis a SQL migration script created for DSpace 5.x (
V5.0) on Sept 26, 2014 (
2014_09_24). Its purpose was to fulfill the needs of ticket DS-1582, which was to migrate the database in order to support adding metadata on all objects.
- More examples can be found under the
- Java migration script naming convention:
V5_0_2014_09_25__DS_1582_Metadata_For_All_Objects_drop_constraint.javais a Java migration created for DSpace 5.x (
V5_0) on Sept 25, 2014 (
2014_09_25). Its purpose was to fulfill the needs of ticket DS-1582, specifically to drop a few constraints.
- More examples can be found under the
- Flyway will execute migrations in order, based on their Version and Date. So, V1.x (or V1_x) scripts are executed first, followed by V3.0 (or V3_0), etc. If two migrations have the same version number, the date is used to determine ordering (earlier dates are run first).
DSpace offers two means for storing content.
- Storage in the file system on the server
- Storage using SRB (Storage Resource Broker)
Both are achieved using a simple, lightweight API.
SRB is purely an option but may be used in lieu of the server's file system or in addition to the file system. Without going into a full description, SRB is a very robust, sophisticated storage manager that offers essentially unlimited storage and straightforward means to replicate (in simple terms, backup) the content on other local or remote storage resources.
The terms "store", "retrieve", "in the system", "storage", and so forth, used below can refer to storage in the file system on the server ("traditional") or in SRB.
The BitstreamStorageManager provides low-level access to bitstreams stored in the system. In general, it should not be used directly; instead, use the Bitstream object in the content management API since that encapsulates authorization and other metadata to do with a bitstream that are not maintained by the BitstreamStorageManager.
The bitstream storage manager provides three methods that store, retrieve and delete bitstreams. Bitstreams are referred to by their 'ID'; that is the primary key bitstream_id column of the corresponding row in the database.
There can be multiple bitstream stores. Each of these bitstream stores can be traditional storage or SRB storage. This means that the potential storage of a DSpace system is not bound by the maximum size of a single disk or file system and also that traditional and SRB storage can be combined in one DSpace installation. Both traditional and SRB storage are specified by configuration parameters. Also see Configuring the Bitstream Store below.
Stores are numbered, starting with zero, then counting upwards. Each bitstream entry in the database has a store number, used to retrieve the bitstream when required.
At the moment, the store in which new bitstreams are placed is decided using a configuration parameter, and there is no provision for moving bitstreams between stores. Administrative tools for manipulating bitstreams and stores will be provided in future releases. Right now you can move a whole store (e.g. you could move store number 1 from /localdisk/store to /fs/anotherdisk/store but it would still have to be store number 1 and have the exact same contents.
Bitstreams also have an 38-digit internal ID, different from the primary key ID of the bitstream table row. This is not visible or used outside of the bitstream storage manager. It is used to determine the exact location (relative to the relevant store directory) that the bitstream is stored in traditional or SRB storage. The first three pairs of digits are the directory path that the bitstream is stored under. The bitstream is stored in a file with the internal ID as the filename.
For example, a bitstream with the internal ID 12345678901234567890123456789012345678 is stored in the directory:
The reasons for storing files this way are:
- Using a randomly-generated 38-digit number means that the 'number space' is less cluttered than simply using the primary keys, which are allocated sequentially and are thus close together. This means that the bitstreams in the store are distributed around the directory structure, improving access efficiency.
- The internal ID is used as the filename partly to avoid requiring an extra lookup of the filename of the bitstream, and partly because bitstreams may be received from a variety of operating systems. The original name of a bitstream may be an illegal UNIX filename.
When storing a bitstream, the BitstreamStorageManager DOES set the following fields in the corresponding database table row:
- The remaining fields are the responsibility of the Bitstream content management API class.
The bitstream storage manager is fully transaction-safe. In order to implement transaction-safety, the following algorithm is used to store bitstreams:
- A database connection is created, separately from the currently active connection in the current DSpace context.
- An unique internal identifier (separate from the database primary key) is generated.
- The bitstream DB table row is created using this new connection, with the deleted column set to true.
- The new connection is _commit_ted, so the 'deleted' bitstream row is written to the database
- The bitstream itself is stored in a file in the configured 'asset store directory', with a directory path and filename derived from the internal ID
- The deleted flag in the bitstream row is set to false. This will occur (or not) as part of the current DSpace Context.
This means that should anything go wrong before, during or after the bitstream storage, only one of the following can be true:
- No bitstream table row was created, and no file was stored
- A bitstream table row with deleted=true was created, no file was stored
- A bitstream table row with deleted=true was created, and a file was stored
None of these affect the integrity of the data in the database or bitstream store.
Similarly, when a bitstream is deleted for some reason, its deleted flag is set to true as part of the overall transaction, and the corresponding file in storage is not deleted.
The above techniques mean that the bitstream storage manager is transaction-safe. Over time, the bitstream database table and file store may contain a number of 'deleted' bitstreams. The cleanup method of BitstreamStorageManager goes through these deleted rows, and actually deletes them along with any corresponding files left in the storage. It only removes 'deleted' bitstreams that are more than one hour old, just in case cleanup is happening in the middle of a storage operation.
This cleanup can be invoked from the command line via the cleanup command, which can in turn be easily executed from a shell on the server machine using
[dspace]/bin/dspace cleanup. You might like to have this run regularly by cron, though since DSpace is read-lots, write-not-so-much it doesn't need to be run very often.
The bitstreams (files) in traditional storage may be backed up very easily by simply 'tarring' or 'zipping' the
[dspace]/assetstore/ directory (or whichever directory is configured in dspace.cfg). Restoring is as simple as extracting the backed-up compressed file in the appropriate location.
Similar means could be used for SRB, but SRB offers many more options for managing backup.
It is important to note that since the bitstream storage manager holds the bitstreams in storage, and information about them in the database, that a database backup and a backup of the files in the bitstream store must be made at the same time; the bitstream data in the database must correspond to the stored files.
Of course, it isn't really ideal to 'freeze' the system while backing up to ensure that the database and files match up. Since DSpace uses the bitstream data in the database as the authoritative record, it's best to back up the database before the files. This is because it's better to have a bitstream in storage but not the database (effectively non-existent to DSpace) than a bitstream record in the database but not storage, since people would be able to find the bitstream but not actually get the contents.
With DSpace 1.7 and above, there is also the option to backup both files and metadata via the AIP Backup and Restore feature.
Configuring the Bitstream Store
Both traditional and SRB bitstream stores are configured in dspace.cfg.
Configuring Traditional Storage
Bitstream stores in the file system on the server are configured like this:
(Remember that [dspace] is a placeholder for the actual name of your DSpace install directory).
The above example specifies a single asset store.
The above example specifies two asset stores. assetstore.dir specifies the asset store number 0 (zero); after that use assetstore.dir.1, assetstore.dir.2 and so on. The particular asset store a bitstream is stored in is held in the database, so don't move bitstreams between asset stores, and don't renumber them.
By default, newly created bitstreams are put in asset store 0 (i.e. the one specified by the assetstore.dir property.) This allows backwards compatibility with pre-DSpace 1.1 configurations. To change this, for example when asset store 0 is getting full, add a line to dspace.cfg like:
Then restart DSpace (Tomcat). New bitstreams will be written to the asset store specified by assetstore.dir.1, which is /mnt/other_filesystem/assetstore_1 in the above example.
Configuring SRB Storage
The same framework is used to configure SRB storage. That is, the asset store number (0..n) can reference a file system directory as above or it can reference a set of SRB account parameters. But any particular asset store number can reference one or the other but not both. This way traditional and SRB storage can both be used but with different asset store numbers. The same cautions mentioned above apply to SRB asset stores as well: The particular asset store a bitstream is stored in is held in the database, so don't move bitstreams between asset stores, and don't renumber them.
For example, let's say asset store number 1 will refer to SRB. The there will be a set of SRB account parameters like this:
Several of the terms, such as mcatzone, have meaning only in the SRB context and will be familiar to SRB users. The last, srb.parentdir.n, can be used to used for addition (SRB) upper directory structure within an SRB account. This property value could be blank as well.
(If asset store 0 would refer to SRB it would be srb.host = ..., srb.port = ..., and so on (.0 omitted) to be consistent with the traditional storage configuration above.)
The similar use of assetstore.incoming to reference asset store 0 (default) or 1..n (explicit property) means that new bitstreams will be written to traditional or SRB storage determined by whether a file system directory on the server is referenced or a set of SRB account parameters are referenced.
There are comments in dspace.cfg that further elaborate the configuration of traditional and SRB storage.