Upgrading NIH VIVO
 
Steps to Upgrade from Version 1 Release 0.9 to Release 1.0

This file provides a short description of the steps involved in upgrading your 
installation of �NIH VIVO� from Version 1 Release 0.9 to Version 1 Release 1.0.

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Before Performing the Upgrade
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The bullet points listed below are important to know before beginning the 
upgrade process. 

The upgrade process is like the original install process with the following 
exceptions:
* DO NOT re-install MySQL or re-create the MySQL database. Please ensure that 
    you back-up the MySQL database.
* It is not necessary to add RDF data, initialize the Lucene Search Index, or 
    re-configure the Apache HTTP Server.
* First-time login of the administrator account will use the password 
    previously set, NOT the password in deploy.properties.
* Any image files that have been uploaded into the system will not be disturbed 
    by the upgrade.
* The first time that Apache Tomcat starts up after the upgrade, it will 
    initiate a process which modifies the data in the model, aligning the data 
    with the revised ontology. For the most part, data in the model will not be 
    lost. See the section on "Ontology Changes" (below) for more information.
* If you make any changes to the application, they should be made in the source 
    directory and deployed, and not made directly within Apache Tomcat.
    
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The Process
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1. Ensure that backups are created of the Tomcat webapps directory, the 
    original source directory, and the MySQL database.

2. Download the new distribution file and unpack it into a new source directory.

3. Create deploy.properties, using the same values as in your original 
    installation. Be aware that deploy.properties now requires an additional 
    property:
       vitro.core.dir = ./vitro-core
    The file example.deploy.properties has been modified to show this. 

4. Apply any changes you have made to the new source directory.

   Note: In many cases, simply copying the modified files from your original 
      source directory will not work since the files on which they are based 
      have changed. It will be necessary to inspect the new source files and 
      add any changes to them at that time.
      
   Note: At a minimum it will be necessary to apply the Google Analytics Tracking 
      code to footer.jsp in the theme:
             [new_source_directory]/themes/[theme_dir]/jsp/footer.jsp
      For additional information and a copy your institution's tracking code, 
        see the Google Analytics wiki page.
        
   Note: Version 1 Release 0.9 contained two directories called "modifications"
      and "ontology". These directories have been combined into a directory 
      called "productMods". If your site has made changes to the ontology 
      ensure that those changes are moved into "productMods".
      
5. If you had modified web.xml to configure the "Pellet Reasoner" (as described
    in the installation instructions), repeat that modification.

6. Run ant deploy by typing: ant

7. Lastly, start "Apache Tomcat" and login to VIVO.

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Ontology Changes
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There are changes in the ontology that may require sites to modify the data in 
their model.

For example, if there is a split in a combined class 
(e.g., SchoolOrCollegeWithinUniversity into School and College) it is 
impossible to determine which class of individuals were added to the combined 
class and which class those individuals should be assigned.

Note: When "Apache Tomcat" starts up following the upgrade, it will initiate 
a process which may modify the data in the model, to align the data to the 
current ontology. Refer to your institutions ontology team representative for 
additional information on ontology changes affecting data prior to performing 
the upgrade.

The ontology alignment process will create these files in the Tomcat webapps directory:
* WEB-INF/ontologies/update/logs/knowledgeBaseUpdate.log 
    a log of updates that were made to the knowledge base and notes about some 
    of the recommended manual reviews.
* WEB-INF/ontologies/update/logs/knowledgeBaseUpdate.error.log 
    a log of errors that were encoundered during the upgrade process.
* WEB-INF/ontologies/update/removedData/removedData.rdf 
    a file containing the stataements that were removed from the data model.
* WEB-INF/ontologies/update/addedData/addedData.rdf 
    a file containing the statements that were added to the data model.
After Apache Tomcat is started, you should review these files to see whether 
you need to edit any data in response to the ontology changes.