Add "upgrade.txt" to the docs directory -- a version-controlled form of the Upgrade document.
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doc/upgrade.txt
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doc/upgrade.txt
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Upgrading NIH VIVO
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Steps to Upgrade from Version 1 Release 0.9 to Release 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 <20>NIH VIVO<56> from version 1 release 0.9 to release 1.0.
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----------
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Before Performing the Upgrade
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----------
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The bullet points listed below are important to know before beginning the
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upgrade process.
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The upgrade process is like the original install process with the following
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exceptions:
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* DO NOT re-install MySQL or re-create 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, initialize the Lucene Search Index, or
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re-configure 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 that Apache Tomcat starts up after the upgrade, it will
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initiate a process which modifies the data in the model, aligning the data
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with the revised ontology. For the most part, data in the model will not be
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lost. See the section on "Ontology Changes" (below) for more information.
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* If you make any changes to the application, they should be made in the source
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directory and deployed, and not made directly within Apache Tomcat.
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----------
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The Process
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----------
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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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Note: Release 0.9 contained two directories called "modifications" and
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"ontology". These directories have been combined into a directory called
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"productMods". If your site has made changes to the ontology ensure that
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those changes are moved into "productMods".
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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. Run ant deploy by typing: ant
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7. Lastly, start "Apache Tomcat" and login to VIVO.
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----------
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Ontology Changes
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----------
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There are changes in the ontology that may require sites to modify the data in
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their model.
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For example, if there is a split in a combined class
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(e.g., SchoolOrCollegeWithinUniversity into School and College) it is
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impossible to determine which class of individuals were added to the combined
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class and which class those individuals should be assigned.
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Note: When "Apache Tomcat" starts up following the upgrade, it will initiate
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a process which may modify the data in the model, to align the data to the
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current ontology. Refer to your institutions ontology team representative for
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additional information on ontology changes affecting data prior to performing
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the upgrade.
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The ontology alignment process will create these files in the Tomcat webapps directory:
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* WEB-INF/ontologies/update/logs/knowledgeBaseUpdate.log
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a log of updates that were made to the knowledge base and notes about some
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of the recommended manual reviews.
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* WEB-INF/ontologies/update/logs/knowledgeBaseUpdate.error.log
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a log of errors that were encoundered during the upgrade process.
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* WEB-INF/ontologies/update/removedData/removedData.rdf
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a file containing the stataements that were removed from the data model.
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* WEB-INF/ontologies/update/addedData/addedData.rdf
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a file containing the statements that were added to the data model.
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After Apache Tomcat is started, you should review these files to see whether
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you need to edit any data in response to the ontology changes.
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