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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 are always stored internally with datatypes. "Untyped" string literals are the same as the identical value typed as xsd:string. See the following document for more information
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Code, tools, parsers, utilities based on RDF 1.0 should not be used with Vitro and VIVO 12.0.100. All code, tools, parsers, and utilities must support RDF 1.1.
On start-up of version 12.0.100, the triple store is checked to insure that it has been upgraded. If untyped literals are found in the triple store, an error message will appear in the browser and the application will not start. The test applies only to the content store. It is possible that your content store could pass this test, but your configuration triple store remains incompatible with Jena 3 and RDF 1.1. In such a case, your application may become unstable. The procedure below will upgrade both your configuration triple store and your content triple store.
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 <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
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2.0.
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Download 12.0.10 0 beta from GitHub. Follow the instructions for installing VIVO. Stop prior to starting Tomcat.
Step 3: Export the triple stores
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To export your triples store, use the jena2tools utility provided with VIVO 12.0.100, in <vivo home dir>/bin, specifying the export command, as shown below.
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jena2tools will then extract the contents of the available triple stores, and dump them to <vivo home dir>/dumps in TriG format.
Step 4: Inspect the dumps
Check <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.
Step 5: Empty your triple stores
Drop all tables in your SDB database as named in your runtime.properties. You may drop your database and recreate it as empty, just as you would for creating a new VIVO install. jena3tools must find an empty database (no tables) as named in your runtime.properties and will recreate your SDB triple store as tables in the named database using the triples produced by jena2tools and stored in <vivo home dir>/dumps/content.trig
Delete all files in <vivo home dir>/tdbModels. Jena3tools will rebuilt your configuration tdbModels based on the content created by jena2tools and stored in <vivo home dir>/dumps/configuration.trig
Step 6: Import the triple stores
Having exported your Jena 2 triple stores, you can reload them using jena3tools, also available with VIVO 12.0.100, specifying the import command.
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jena3tools will be present in <vivo home dir>/bin when you install the 12.100.0 beta0 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
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After upgrading, does the application behave as expected? Can you see everything in VIVO, log in, edit content, use the system admin pages, see visualizations, conduct searches, etc.
Reporting
If you are testing the Vitro / VIVO beta release, please report your findings:
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Please report your findings on the vivo-tech@googlegroups.com mailing list.
Files
https://github.com/vivo-project/VIVO/releases
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