NIHVIVO-511 start the 1.1 upgrade document.
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doc/upgrade-1.0.txt
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-------------------------------------------------------------------------------
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Upgrading NIH VIVO
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Steps to Upgrade from Release 1 Version 0.9 to Release 1 Version 1.0
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This file provides a short description of the steps involved in upgrading your
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installation of NIH VIVO from Release 1 Version 0.9 to Release 1 Version 1.0.
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This and other documentation can be found at:
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http://vivoweb.org/support
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Installation:
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If you need to do a fresh install, please consult the install.txt in this
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directory.
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-------------------------------------------------------------------------------
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I. Before Performing the Upgrade
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II. The Upgrade Process
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III. Ontology Changes
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-------------------------------------------------------------------------------
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I. Before Performing the Upgrade
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Please read the bullet points below BEFORE beginning the upgrade.
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The upgrade process is similar to the original install process with the following
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exceptions:
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* DO NOT reinstall MySQL or recreate the MySQL database. Please ensure that
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you back-up the MySQL database.
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* It is not necessary to add RDF data or reconfigure the Apache HTTP Server.
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* First-time login of the administrator account will use the password
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previously set, NOT the password in deploy.properties.
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* Any image files that have been uploaded into the system will not be disturbed
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by the upgrade.
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* The first time Apache Tomcat starts up after the upgrade, it will
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initiate a process that modifies the knowledge base to align the data
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with the revised ontology. See the section on "Ontology Changes"
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below for more information.
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-------------------------------------------------------------------------------
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II. The Upgrade Process
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1. Ensure that backups are created of the Tomcat webapps directory, the
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original source directory, and the MySQL database.
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2. Download the new distribution file and unpack it into a new source directory.
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3. Create deploy.properties, using the same values as in your original
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installation. Be aware that deploy.properties now requires an additional
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property:
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vitro.core.dir = ./vitro-core
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The file example.deploy.properties has been modified to show this.
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4. Apply any changes you have made to the new source directory.
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Note: In many cases, simply copying the modified files from your original
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source directory will not work since the files on which they are based
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have changed. It will be necessary to inspect the new source files and
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add any changes to them at that time.
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Note: At a minimum it will be necessary to apply the Google Analytics Tracking
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code to footer.jsp in the theme:
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[new_source_directory]/themes/[theme_dir]/jsp/footer.jsp
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For additional information and a copy your institution's tracking code,
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see the Google Analytics wiki page.
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https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI
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Note: Version 1 Release 0.9 contained two directories called "modifications"
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and "ontology". These directories have been combined into a directory
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called "productMods". If your site has made changes to the ontology
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ensure that those changes are moved into the appropriate subdirectory of
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"productMods".
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Note: This process assumes any changes made to the application were made in
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the source directory and deployed, and were not made directly within
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Apache Tomcat webapp.
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5. If you had modified web.xml to configure the Pellet Reasoner (as described
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in the installation instructions), repeat that modification.
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6. Stop "Apache Tomcat" and run ant deploy by typing: ant deploy
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7. If you have setup the Apache Tomcat Connector using mod_jk and modified your
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tomcat/conf/server.xml file, you will need to add 4 lines to your context
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section, see examples below.
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Context section before:
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<Context path=""
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docBase="/usr/local/tomcat/webapps/vivo"
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reloadable="true"
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cookies="true" >
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</Context>
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Context section after:
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<Context path=""
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docBase="/usr/local/tomcat/webapps/vivo"
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reloadable="true"
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cookies="true" >
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<Environment type="java.lang.String" override="false"
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name="path.configuration"
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value="deploy.properties"
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/>
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</Context>
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Also, if you have these 3 lines in your Apache virtual host configuration,
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please remove them!
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<Location "/edit/forms">
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deny from all
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<Location>
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8. Start "Apache Tomcat" and login to VIVO.
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9. Rebuild the Lucene search index as described in step IX of
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the install process. This step will ensure that changes in the RDF
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data to align with the latest version of the core ontology
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will be reflected in the search index.
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-------------------------------------------------------------------------------
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III. Ontology Changes
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Changes to the VIVO core ontology may require corresponding
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modifications of the knowledge base instance data and local ontology
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extensions.
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When Apache Tomcat starts up following the upgrade, it will initiate
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a process to examine the knowledge base and apply necessary changes.
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Not all of the modifications that may be required can be automated,
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so manual review of the knowledge base is recommended after the
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automated upgrade process. The automated process will make only
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the following types of changes:
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Class or Property renaming
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All references to the class (in the subject or object position) will
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be updated to the new name. References to the property will be
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updated to the new name.
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Class or Property deletion
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All individuals in a deleted class will be changed to
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belong to the nearest available superclass (which may be owl:Thing).
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All statements using a deleted property will be changed
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to use the nearest available superproperty. If there is no available
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superproperty then the statement will be deleted from the
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knowledge base. Note that all removed and added data
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is recorded in the files in the changedData directory.
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Class or Property addition
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If a newly added class has a superclass and there are
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individuals in that superclass, then a note will be
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added to the log file suggesting review of those individuals to
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see if they should be reasserted in the newly added class.
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If a newly added property has a superproperty and there are
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statements using the superproperty, then a note will be added to
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the log file suggesting review of those statements to see if they
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should be reasserted using the newly added property.
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Annotation property default values
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It a site has modified the value of a vitro annotation (such as
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displayRankAnnot or displayLimitAnnot) so that it is
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no longer using the default, then that setting will be left unchanged.
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If a site is using the default value of a vitro annotation, and the
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default has been changed in the new version of the ontology, then
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the new default value will be propagated to the knowledge base.
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The ontology alignment process will create the following files in the
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Tomcat webapps/vivo/WEB-INF directory:
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ontologies/update/logs/knowledgeBaseUpdate.log
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a log of a summary of updates that were made to the knowledge base and notes
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about some recommended manual reviews. This file should end with
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"Successfully finished processing ontology changes".
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ontologies/update/logs/knowledgeBaseUpdate.error.log
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a log of errors that were encountered during the upgrade process. This file
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should be empty if the upgrade was successful.
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ontologies/update/changedData/removedData.n3
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an N3 file containing all the statements that were removed from the knowledge base.
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ontologies/update/changedData/addedData.n3
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an N3 file containing all the statements that were added to the knowledge base.
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After Apache Tomcat is started, these files should be reviewed to verify that
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the automated upgrade process was executed successfully.
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