The upgrade-1.2.html is up2date with the content in upgrade-1.2.txt, so I will ask developers to edit upgrade-1.2.html
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-------------------------------------------------------------------------------
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Upgrading VIVO
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Steps to Upgrade from Release 1 Version 1.1.1 to Release 1 Version 1.2
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This file provides a short description of the steps involved in upgrading your
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installation of VIVO from Release 1 Version 1.1.1 to Release 1 Version 1.2.
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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 Upgrade
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A. Verify Ontology upgrade process
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B. Ontology knowledge base manual review
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IV. Theme 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.
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* First-time login of the administrator account after the upgrade process is
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complete will use the password previously set, NOT the default password used
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on the first login after the initial installation.
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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 Upgrade"
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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, the MySQL database, and the uploaded files
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directory (images).
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2. Download the new distribution file and unpack it into a new source
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directory.
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3. Create deploy.properties, using the same values as in your previous
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installation.
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4. Apply any previous changes you have made to the new source directory.
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************* Special notes regarding source files ********************
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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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the Tomcat webapps directory.
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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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At a minimum it will be necessary to apply the Google Analytics Tracking
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Code (GATC) to googleAnalytics.ftl in the theme:
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[new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl
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A sample googleAnalytics.ftl is included in the built-in theme. This file
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serves only as an example, and you must replace the tracking code shown
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with your institution's own tracking code.
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For additional information about the GATC for the NIH-funded VIVO
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implementation sites and a copy your institution's tracking code, see the
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VIVO Google Analytics wiki page:
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https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI
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If you had used the vivo/contrib/FLShibboleth code in your previous release,
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you should stop using it. Consult install.txt for instructions on
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"Using an External Authentication System with VIVO".
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************************************************************************
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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 by typing: ant all
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7. Start "Apache Tomcat" and log in to VIVO.
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-------------------------------------------------------------------------------
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III. Ontology Changes
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A. Verify Ontology upgrade process
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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. The ontology alignment
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process will create the following files in the 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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B. Ontology knowledge base manual review
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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 removed.
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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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Property addition
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If a newly added property is the inverse of a previously
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existing property, the inverse of any statements using the
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pre-existing property will be asserted.
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Annotation property default values
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If 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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-------------------------------------------------------------------------------
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IV. Theme Changes
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VIVO 1.1 introduces the first step in a transition from JavaServer Pages (JSPs)
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to the FreeMarker template engine for generating web pages. As part of this
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process, the JSP files that were used for theme customization in earlier
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versions of VIVO have been replaced by a set of FreeMarker templates.
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In the 1.1 install package, these files are located in
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/vivo/themes/vivo-basic/templates and have an ftl (for FreeMarker Template
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Language) extension.
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Follow step A or B below, whichever is applicable to your site:
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A. If you did not create a customized theme for your site in VIVO 1.0, but used
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the 1.0 vivo-basic theme in its original directory, you need not take any
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action in order to convert your site to the VIVO 1.1 theme.
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B. If you created your own theme directory in VIVO 1.0, follow the steps below
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under sections "Templates," "Stylesheets," and "Site Icons" to upgrade your
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theme to VIVO 1.1.
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1. Templates
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a. Copy the directory /vivo/themes/vivo-basic/templates into your theme
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directory /vivo/themes/<your-theme-name>.
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b. Follow step i or ii below, whichever is applicable to your theme.
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i. If you did not apply any customizations to the JSPs in your VIVO
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1.0 theme, then you do not need to apply any additional changes
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to the VIVO 1.1 theme templates during the upgrade process.
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ii. If you did apply customizations to the JSPs in your VIVO 1.0
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theme,you will need to hand-replicate those modifications in the
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new theme template files.
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The theme template content that was previously contained in
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three JSP files is now contained in five FTL files. The
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correspondence between the 1.0 JSPs and the 1.1 FTLs is as
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follows:
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identity.jsp => identity.ftl
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menu.jsp => menu.ftl and search.ftl
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footer.jsp => footer.ftl and googleAnalytics.ftl
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googleAnalytics.ftl is a new file to which you will add
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your site's Google Analytics Tracking Code (see section II).
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Because the FreeMarker Template Language uses many syntactic
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conventions that will be familiar to template authors from JSP
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or other common templating systems, the translation of your JSP
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changes into the new FTLs should be relatively straightforward.
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Consult the FreeMarker Template Author's Guide at
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http://freemarker.org/docs/dgui.html and the Reference at
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http://freemarker.org/docs/ref.html for complete documentation
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of the syntax and available built-in constructs. Template
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authors need not be concerned with the Programmer's Guide or
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Java API documentation.
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c. Remove the jsp directory from your themes directory.
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2. Stylesheets
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VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified
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styles in your VIVO 1.0 theme, you will not be able to simply copy the
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1.0 stylesheets into your 1.1 theme, because you will then lose 1.1
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style upgrades that your theme should pick up. Instead, you should
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use the vivo-basic 1.1 stylesheets as a starting point, and manually
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merge your 1.0 style modifications in as needed.
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3. Site Icons
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Copy the site icons from your 1.0 theme into the site_icons folder in
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your 1.1 theme.
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