vivo/doc/upgrade-1.1.1.txt

-------------------------------------------------------------------------------

Upgrading VIVO
 
Steps to Upgrade from Release 1 Version 1.1 to Release 1 Version 1.1.1

This file provides a short description of the steps involved in upgrading your 
installation of VIVO from Release 1 Version 1.1 to Release 1 Version 1.1.1.
For upgrades from V1.0 to V1.1.1 please see the upgrade-1.1.txt file.
This and other documentation can be found at:

http://vivoweb.org/support

Installation:
If you need to do a fresh install, please consult the install.txt in this 
directory.

-------------------------------------------------------------------------------

I.   Before Performing the Upgrade
II.  The Upgrade Process
III. Ontology
IV.  File Storage System
V.   Theme Changes

-------------------------------------------------------------------------------

I. 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:

* DO NOT reinstall MySQL or recreate the MySQL database. Please ensure that 
    you back-up the MySQL database.
* It is not necessary to add RDF data.
* First-time login of the administrator account after the upgrade process is 
    complete will use the password previously set, NOT the default password used 
    on the first login after the initial installation.
         
-------------------------------------------------------------------------------

II. 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.

    ************* Special notes regarding source files ********************
    
    This process assumes any changes made to the application were made in 
       the source directory and deployed, and were not made directly within 
       the Tomcat webapps directory.
       
    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.

    For NIH-funded institutions:
       At a minimum it will be necessary to apply the Google Analytics Tracking 
       Code (GATC) to googleAnalytics.ftl in the theme:
      
      [new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl
      
      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.
      
      For additional information about the GATC for the NIH-funded VIVO 
      implementation sites and a copy your institution's tracking code, see the 
      VIVO Google Analytics wiki page:
      https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI
      
   ************************************************************************     
      
5. If you had modified web.xml to configure the Pellet Reasoner (as described
    in the installation instructions), repeat that modification.

6. Stop "Apache Tomcat" and run ant by typing: ant all

7. If you have set up the Apache Tomcat Connector using mod_jk and modified 
	your tomcat/conf/server.xml file, there are no changes in this upgrade. 
	For upgrades from V1.0 to V1.1.1, please see the upgrade-1.1.txt file.  
	
8.  VIVO is a multithreaded web application that may require more threads than 
    are permitted under your Linux installation's default configuration. Ensure 
    that your installation can support the required number of threads by making 
    the following edits to /etc/security/limits.conf:

    apache    hard    nproc   400
    tomcat6   hard    nproc   1500 

9. Start "Apache Tomcat" and log in to VIVO.

-------------------------------------------------------------------------------

III. Ontology Changes

There are some minor changes to the ontology with the V1.1.1 upgrade, but there 
is no data migration occurring.  For upgrades from V1.0 to V1.1.1, please see the 
upgrade-1.1.txt file.  

-------------------------------------------------------------------------------

IV. File Storage System

There are no changes to the file storage system with the upgrade from V1.1
to V1.1.1. For changes related to upgrading from V1.0 to V1.1.1, 
please see the upgrade-1.1.txt file.

-------------------------------------------------------------------------------

V. Theme Changes

Follow step A or B below, whichever is applicable to your site:

A. If you did not create a customized theme for your site in VIVO 1.0, but used
the 1.0 vivo-basic theme in its original directory, you need not take any 
action in order to convert your site to the VIVO 1.1 theme.

B. If you created your own theme directory in VIVO 1.1, you can copy it back
into the theme directory location: /vivo/themes/*

If you are upgrading from V1.0 to V1.1.1, please see the upgrade-1.1.txt file.