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+
+-------------------------------------------------------------------------------
+
+Upgrading VIVO
+
+Steps to Upgrade from Release 1 Version 1.0 to Release 1 Version 1.1
+
+This file provides a short description of the steps involved in upgrading your
+installation of VIVO from Release 1 Version 1.0 to Release 1 Version 1.1.
+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.
+* The first time Apache Tomcat starts up after the upgrade, it will
+ initiate a process that modifies the knowledge base to align the data
+ with the revised ontology. See the section on "Ontology Upgrade"
+ below for more information.
+* The first time Apache Tomcat starts up after the upgrade, it will
+ initiate a process that modifies the uploaded files directory (images), to
+ align the uploaded files with the revised file storage scheme. See the
+ section on "File Storage Changes" below for more information.
+
+-------------------------------------------------------------------------------
+
+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.
+
+ 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, you will need to add a line to your
+ context section specifying a "Manager" tag; see examples below.
+
+ Context section before:
+
+
+
+
+
+ Context section after:
+
+
+
+
+
+
+8. 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.
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