Database Preservation

Relational databases are one of the most important technologies supporting today’s information management activities. They are designed to store, organize and explore digital records that not only support but also document day-to-day business operations. Very often, these records are irreplaceable or prohibitively expensive to reacquire by other means rendering the preservation of databases a serious concern.

This page focus on workflows, tools and standards to allow information managers to extract, archive and preserve records of information currently managed by relational databases.

The most relevant initiatives in this context are the Database Preservation Toolkit, the Database Visualization Toolkit and the SIARD 2.0 preservation format.

The following screencast aims to illustrate how all these tools fit together in a full-cycle archiving and preservation workflow for relational databases.

More detailed information about these tools and standards can be found on the following sections.

RODA – A digital repository made for preservation

RODA is a complete digital repository solution that delivers functionality for all the main functional units of the OAIS reference model. RODA is capable of ingesting, managing and providing access to the various types of digital content produced by large corporations or public bodies. RODA is based on open-source technologies and is supported by existing standards such as the Open Archival Information System (OAIS), Metadata Encoding and Transmission Standard (METS), Encoded Archival Description (EAD), Dublin Core (DC) and PREMIS (Preservation Metadata).

For more information please visit https://github.com/keeps/roda

RODA-in – The ultimate SIP creation tool

RODA-in is a tool specially designed for producers and archivists to create Submission Information Packages (SIP) ready to be submitted to an Open Archival Information System (OAIS). The tool creates SIPs from files and folders available on the local file system.

In version 2 we revolutionized the way SIPs are created to satisfy the need for mass processing of data. In this version you can create thousands of valid SIPs with just a few clicks, complete with data and metadata.

The tool includes features such as:

For more information please visit https://github.com/keeps/roda-in

Database Preservation Toolkit

The Database Preservation Toolkit allows conversion between Database formats, including connection to live systems, for purposes of digitally preserving databases. The toolkit allows conversion of live or backed-up databases into preservation formats such as SIARD, a XML-based format created for the purpose of database preservation. The toolkit also allows conversion of the preservation formats back into live systems to allow the full functionality of databases.

This toolkit was part of the RODA project and now has been released as a project by its own due to the increasing interest on this particular feature. It is now being further developed in the EARK project together with a new version of the SIARD preservation format.

The toolkit is created as a platform that uses input and output modules. Each module supports read and/or write to a particular database format or live system. New modules can easily be added by implementation of a new interface and adding of new drivers.

EARK and SIARD 2.0

A new version of the this tool, together with a new version of the SIARD preservation format, is currently being designed and developed on the EARK project. Meanwhile, if you'd like to know more and even send us use cases and requirements, contact us.

Database Visualization Toolkit

The Database Visualization Toolkit is a lightweight web viewer for relational databases, specially if preserved in SIARD 2, that uses SOLR as a backend, and allows browsing, search, and export. It uses the Database Preservation Toolkit to process new relational databases that are in the SIARD2 format or on the original live DBMS.

For more information please visit http://visualization.database-preservation.com

How to use

To use the program, open a command-line and try out the following command (replace x.y.z accordingly to the version of the binary in use):

$ java -jar dbptk-app-X.Y.Z.jar

Using this command you will be presented with the application usage, describing all supported modules and their parameters. This information is also available in the application usage page.

To use the application an input and an output module must be selected and some configuration parameters must be provided.

Supported Database Management Systems and Preservation formats

The Database Preservation Toolkit supports the following Database Management Systems:

Database Preservation Toolkit can convert any of the above DBMS to the following preservation formats:

The Database Preservation Toolkit is also capable of loading preserved databases into any of the above DBMS.

Examples

If you want to connect to a live MySQL database and export its content to SIARD 2.0 format, you can use the following command.

$ java -jar dbptk-app-x.y.z.jar \
--import mysql --import-hostname=localhost --import-database="example_db" --import-username=username --import-password="p4ssw0rd" \
--export siard-2 --export-file=example.siard

Or using the equivalent short version of the parameters:

$ java -jar dbptk-app-x.y.z.jar \
-i mysql -ih localhost -idb "example_db" -iu username -ip "p4ssw0rd" \
-e siard-2 -ef example.siard

More examples containing only required parameters:

Oracle to SIARD 2

$ java -jar dbptk-app-x.y.z.jar \
--import oracle --import-server-name=127.0.0.1 --import-database="example_db" --import-username=username --import-password="p4ssw0rd" --import-accept-license \
--export siard-2 --export-file=example.siard

MySQL to SIARD 2

$ java -jar dbptk-app-x.y.z.jar \
--import mysql --import-hostname=localhost --import-database="example_db" --import-username=username --import-password="p4ssw0rd" \
--export siard-2 --export-file=example.siard

PostgreSQL to SIARD 2

$ java -jar dbptk-app-x.y.z.jar \
--import postgresql --import-hostname=localhost --import-database="example_db" --import-username=username --import-password="p4ssw0rd" \
--export siard-2 --export-file=example.siard

Microsoft SQL Server to SIARD 2

$ java -jar dbptk-app-x.y.z.jar \
--import microsoft-sql-server --import-server-name=localhost --import-database="example_db" --import-username=username --import-password="p4ssw0rd" \
--export siard-2 --export-file=example.siard

The conversion in the opposite direction is also possible, check the complete application usage to know more about the supported modules and respective configurations.

How to use JDBC import and export modules

To use Database Preservation Toolkit with an unsupported database, one can connect by providing the name of the JDBC driver class (and adding the JDBC driver to the classpath) and the JDBC connection string. The steps to run Database Preservation Toolkit this way are as follows:

  1. Obtain the JDBC driver for the database you want to use (this is typically a file with jar extension). For Oracle12C this file can be downloaded from http://www.oracle.com/technetwork/database/features/jdbc/index-091264.html;
  2. Identify the driver class. For Oracle 12C this would be something like oracle.jdbc.driver.OracleDriver;
  3. Prepare the connection string. For Oracle 12C this could be something like jdbc:oracle:thin:username/password@serverName:port/database;
  4. Run Database Preservation Toolkit by providing files to add to the classpath and the main entry point.

Please be aware that using this method the conversion quality cannot be assured, as it depends on the used driver. Furthermore, non-tested drivers are more prone to possible errors during the conversion. A specialized module for the database, if available, would always be preferable to this generic JDBC module.

Example to convert from Oracle to SIARD2:

Using the method described above, the Windows command to extract a database from an Oracle database to SIARD 2 is as the following:

java -cp "C:\path\to\dbptk-app-x.y.z.jar;C:\path\to\jdbc_driver.jar" com.databasepreservation.Main \
  --import=jdbc --import-driver=oracle.jdbc.driver.OracleDriver \
    --import-connection="jdbc:oracle:thin:username/password@serverName:port/database" \
  -e siard-2 -ef C:\path\to\output.siard

And on Linux the equivalent command would be (note that the jarfile separator is : instead of ;):

java -cp "/path/to/dbptk-app-x.y.z.jar:/path/to/jdbc_driver.jar" com.databasepreservation.Main \
  --import=jdbc --import-driver=oracle.jdbc.driver.OracleDriver \
    --import-connection="jdbc:oracle:thin:username/password@serverName:port/database" \
  -e siard-2 -ef /path/to/output.siard

How to build from source

  1. Download the latest stable release.
  2. Unzip and open the folder on a command-line terminal
  3. Build with Maven mvn clean package

Binaries will be on the target folder

Related publications & presentations

Other related publications:

Troubleshooting

Getting exception "java.net.ConnectException: Connection refused"

Most databases are not configured by default to allow TCP/IP connections. Check your database configuration if it accepts TCP/IP connection and if your IP address is allowed to connect. Also, ensure that the user has permissions to access the database from your IP address.

Problems importing from Microsoft Access

To import from Microsoft Access you need to be on a Windows machine with Microsoft Access installed. This is because the current Microsoft Access import module is implemented using ODBC connection. Therefore, you need Windows installed to be able to use ODBC. Also, you need Microsoft Access installed so its ODBC driver is installed on your system.

Furthermore, in order to extract DB structures we need to have access to the internal database table Msysrelationships. You need to perform some hacking over the DBMS and this is version dependent. Please follow the instructions described on Microsoft's white paper, which explains how to do this for all Microsoft Access versions: "Preparing a Microsoft Access Database for Migration".

Got error "java.lang.OutOfMemoryError: Java heap space"

The toolkit might need more memory than it is available by default (normally 64MB). To increase the available memory use the -Xmx option. For example, the following command will increase the heap size to 3 GB.

$ java -Xmx3g -jar dbptk-app-x.y.z.jar ...

The toolkit needs enough memory to put the table structure definition in memory (not the data) and to load each data row or row set, which might include having some BLOBs completely in memory, but this depends on the database driver implementation.

Main hard drive gets full due to temporary files

Due to the structure of some export modules (e.g. SIARD) and because we only want to pass throught the database once with minimum amount of used memory, all BLOBs and CLOBs of a database table must be kept on temporary files during the export of a table. This can cause your main disk to get full and the execution to fail. To select a diferent folder for the temporary files, e.g. on a bigger hard drive, use the option -Djava.io.tmpdir=/path/to/tmpdir. For example, the following command will use the folder /media/BIGHD/tmp as the temporary folder:

$ java -Djava.io.tmpdir=/media/BIGHD/tmp -jar dbptk-app-x.y.z.jar ...

Information & Commercial support

For more information or commercial support, contact KEEP SOLUTIONS.

Development Build Status

To develop we recommend the use of Maven and Eclipse (or Intellij with Eclipse Code Formatter plugin).

The following plugins should be installed in Eclipse:

And the following environment variables should be set:

To run PostgreSQL tests, a local PostgreSQL database is required and postgres user or another user with permission to create new databases and users can be used. This user must be accessible by IP connection on localhost. The access can be tested with psql -U username -h 127.0.0.1 -d postgres -W.

To run MySQL tests, a local MySQL (or MariaDB) database is required and 'root' user or another user with permission to create new databases and users can be used. This user must be accessible by IP connection on localhost. The access can be tested with mysql --user="username" -p --database="mysql" --host="127.0.0.1".

Building common parts that may be used by other projects

Use mvn clean install -Pcommon to locally install the common artifacts so they can be used by other projects. Note that this is not necessary unless you do not have access to KEEPS Artifactory or you want to make changes to the common artifacts to use in other projects.

Changing XML Schema files

After changing SIARD XML Schema files, maven must be used to compile a new artifact from the XML Schema (using JAXB). To do this, run mvn clean install -Pdbptk-bindings from project root folder. This will install the artifacts locally and they will be used instead of the ones in KEEPS Artifactory.

License

Database Preservation Toolkit licence is LGPLv3

                   GNU LESSER GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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