The next major release of Vitro / VIVO contains an upgrade of Jena - from 2.10.1, to Jena 3.x (3.1.1 at time of writing). Whilst development is still progressing, in order to maximise amount of testing of this core upgrade, a beta has been released.
The procedure here describes testing an upgrade from an earlier version of VIVO. If you have questions, please post to vivo-tech@googlegroups.com
What has changed
Jena 3 improves Jena's RDF 1.1 compatibility. Specifically, literal values always have datatypes. "Untyped" string literals are the same as the identical value typed as xsd:string. See the following document for more information
https://jena.apache.org/documentation/migrate_jena2_jena3.html
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Upgrade procedure
It is required that you reload any SDB and TDB triple stores when upgrading to Jena 3 using the procedure and tools described below.
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VIVO/Vitro uses two triple stores – a configuration triple store typically stored using TDB in <home><vivo home dir>/tdbModels, and a content triple store typically stored using SDB in MySQL. The procedures described below assume that you are running this standard configuration. If you are not, you will need a custom procedure for upgrading your triple stores. |
Step 1: Shutdown Tomcat
Use your local procedure for shutting down Tomcat. Tomcat must be shut down for the upgrade process to proceed.
Step 2: Install VIVO 1.10
Download 1.10 beta from GitHub. Follow the instructions for installing VIVO. Stop prior to starting Tomcat.
Step 3: Export the triple stores
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First you need to export your existing Jena 2 triple stores. To do so, shutdown Tomcat, and To export your triples store, use the jena2tools utility provided with VIVO 1.10, in <vivo home dir>/bin, specifying the export command, as shown below.
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java -jar jena2tools.jar -d <vivo home dir> -e |
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On execution, the program will read your configuration files, find your Vitro or VIVO configuration within the vivo/vitro home directory, and get the necessary information to connect to your configuration triple store (usually <home><vivo home dir>/tdbModels), and your content triple store (usually in SDB). If your triple store(s) are not SDB or TDB backed, then it will simply skip them.
It jena2tools will then extract the contents of the available triple stores, and dump them to <vivo home dir>/dumps in TriG format.jena2tools will be present in <vivo home dir>/bin when you install the 1.10.0 beta. Alternatively, it can be downloaded from GitHub.
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4: Inspect the dumps
Check <home><vivo home dir>/dumps to confirm that the triple stores have been exported. Inpect the dump files to insure they contain the data from your triple stores.
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5: Empty your triple stores
Drop all tables in your SDB schema
Delete all files in <home><vivo home dir>/tdbModels
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6: Import the triple stores
Having exported your Jena 2 triple stores, you can reload them using jena3tools, also available with VIVO 1.10, specifying the import command.
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jena3tools will be present in <home><vivo home dir>/bin when you install the 1.10.0 beta. Alternatively, it can be downloaded from GitHub.
Step 7: Start Tomcat
Using your normal procedure, start Tomcat. Perform your usual start-up tests – login, view pages, conduct searches, examine visualizations, perform queries. Please report your findings to vivo-tech@googlegroups.com
Testing notes
The most important thing to test is the upgrade process of Jena 2 to Jena 3. After upgrading, does the application behave as expected? Can you see everything in VIVO, log in, edit content, etc.
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- What version of Vitro / VIVO you upgraded from?
- What storage was used for the content triple store (SDB or TDB)?
- Did it work as expected? If not, what happened?
You can either Please report your findings on the the vivo-tech mailing list, or send them directly to Graham Triggstech@googlegroups.com mailing list.
Files
https://github.com/vivo-project/VIVO/releases
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