Introduction

This file provides a short description of the steps involved in upgrading your installation of VIVO from version 1.0 to 1.1. This and other documentation can be found at: linktovivoweb linktosourceforge. For a new installation, be sure to see the installation document on VIVOWeb or SourceForge.

Before performing the upgrade

Please read the bullet points below before beginning the upgrade. The upgrade process is similar to the original install process with the following exceptions:

The upgrade process

  1. Ensure that backups are created of the Tomcat webapps directory, the original source directory, the MySQL database, and the uploaded files directory (images).
  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 previous installation.
  4. Apply any previous changes you have made to the new source directory.
  5. Special notes regarding source files:
    1. This process assumes any changes made to the application were made in the source directory and deployed, and were not made directory within the Tomcat webapps directory.
    2. 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.
    3. At a minimum, it will be necessary to apply the google analytics tracking code (GATC) to googleAnalytics.ftl in the theme: 
      1. [new source directory]/themes/[theme_dir]/templates/googleAnalytics.ftl
      2. A sample googleAnalytics.ftl is included in the built-in theme. This file serves only as an example, and you must replace the tracking code shown with your institution's own tracking code
      3. For more information about the GATC for the NIH-funded VIVO and a copy of your institution's tracking code, see the Google Analytics wiki page: https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI
  6. If you had a modified web.xml to configure the Pellet Reasoner (as described in the Installation Instructions), repeat that modification.
  7. Stop Apache Tomcat and use ant to build and deploy the new code using 
    ant all
    at the command line.
  8. If you have set up the Apache Tomcat Connector using mod_jk and modified your tomcat/conf/server.xml file, you will need to add a line to your context section specifying a "Manager" tag. See examples below:
    1. Context Section Before 
      <Context Path=""
    docBase="/usr/local/tomcat/webapps/vivo"
    reloadable="true"
    cookies="true">
    <Environment type ="java.lang.String" override="false"
        name="path.configuration"
        value="deploy.properties"
    />
</Context>
    2. Context Section After 
      <Context Path=""
    docBase="/usr/local/tomcat/webapps/vivo"
    reloadable="true"
    cookies="true">
    <Manager pathname="" />
    <Environment type ="java.lang.String" override="false"
        name="path.configuration"
        value="deploy.properties"
    />
</Context>
  9. Start Apache Tomcat and log into VIVO.

Ontology Upgrade

Verify Ontology Upgrade Process

After Apache Tomcat is started, these files should be reviewed to verify that the automated upgrade process was executed successfully. The ontology alignment process will create the following files in the Tomcat webapps/vivo/WEB-INF directory:

Ontology knowledge base manual review

Changes to the VIVO core ontology may require corresponding modifications of the knowledge base instance data and local ontology extensions.

When Apache Tomcat starts up following the upgrade, it will initiate to examine the knowledge base and apply necessary changes.

Not all of the modifications that may be required can be automated; so manual review of the knowledge base is recommended after the automated upgrade process. The automated process will make only the following types of changes:

New file storage system

Verifying the file storage upgrade

If, for any reason, the file storage upgrade process is not successful, no uploaded images will be displayed for individuals. Tomcat's "vivo.all.log" file will contain an exception listing with more information.

The file storage upgrade process wil create these files in the VIVO upload director:

File Storage Changes