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  1. Stop Tomcat - it is vital that Tomcat / VIVO, and any other applications that may access the triple stores, are not running during this process.

  2. Run "mvn clean install -s <your-settings.xml>"  in your VIVO 1.10.0 development area to update your web application and home directory
    This will install the tools into your <vivo_home>/bin directory. Alternatively, you can download jena2tools.jar and jena3tools.jar from this page.

  3. Export your existing triple stores:

    • To export successfully, you need to ensure no other programs are accessing your triple stores.
    • Your file system must have the space available and be capable of storing files large enough to contain your entire triple store serialisation.

    To export your triples store, use the jena2tools utility provided with VIVO 1.10.0, in <vivo home dir>/bin, specifying the export command, as shown below.

    Code Block
    java -jar jena2tools.jar -d <vivo home dir> -e


    -d - the location of the Vitro/VIVO home directory

    -e - run in export mode

    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 <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.

    jena2tools will then extract the contents of the available triple stores, and dump them to <vivo home dir>/dumps in TriG format.


    In rare cases jena2tools will fail with a java.lang.NullPointerException. This can occur if VIVO was not properly shut down before upgrading.

    The preferred fix for this is to restore VIVO 1.9.x and see that it is properly started and shut down before upgrading. If this is not practical, another workaround is to delete the file named tdbModels/journal.jrnl in the Vitro/VIVO home directory. This may result in the loss of the most recent information.

  4. Check that the export has completed - you should have a <vivo_home>/dumps directory, that contains the files "configuration.trig" and "content.trig".

  5. Empty your triple stores ready for reloading:

    Content Triple Store:
    Drop all tables in your SDB database as named in your  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 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

    In MySQL, DROP TABLE Nodes; DROP TABLE Quads; DROP TABLE Triples; DROP TABLE Prefixes;
    - OR - DROP DATABASE <vivodb>; CREATE DATABASE <vivodb> CHARACTER SET utf8mb4; GRANT ALL ON <vivodb>.* TO '<user>'@'localhost';
    - OR - if using a TDB content triple store: rm -rf <vivo_home>/tdbContentModels

    Configuration Triple Store:
    Delete all files in <vivo home dir>/tdbModels.  Jena3tools will rebuild your configuration tdbModels based on the content created by jena2tools and stored in <vivo home dir>/dumps/configuration.trig
    rm -rf <vivo_home>/tdbModels

  6. Reload the data

    Having exported your Jena 2 triple stores, you can reload them using jena3tools, also available with VIVO 1.10.0, specifying the import command.

    Code Block
    java -jar jena3tools.jar -d <vivo home dir> -i


    -d - the location of the Vitro/VIVO home directory

    -i - run in import mode

    On execution, the program will find your Vitro or VIVO configuration within the home directory, as well as the dumps that you have created with jena2tools. It will import them into the SDB and TDB triple stores, based on the configuration of your Vitro/VIVO instance.

    jena3tools will be present in <vivo home dir>/bin when you install the 1.10.0 beta. Alternatively, it can be downloaded from GitHub.

    - Note that this can take a while. A rough guide is to expect about 600 triples per second to reload. (Roughly 1 hour per 2 million triples).

  7. Restart Tomcat

    - Note that there are a couple of spelling mistakes that have been corrected in the filegraphs. As a result, you should expect that VIVO will reinference and re-index the data when you start it up for the first time.