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VIVO Release 1 v1.2 Upgrade Guide

- January 28, 2011 - Upgrading from Release 1 v1.1 to Release 1 v1.2 -
- Missing pieces and fixes - -
- - - -

- This document provides a short description of the steps involved in upgrading your - installation of VIVO from Release 1, Version 1.1 to Version 1.2. This and other - documentation can be found on the support page - at VIVOweb.org -

-

- If you need to do a fresh install, please consult - VIVO Release 1 v1.2 Installation Guide - or the install.html file located in the - - doc - - directoy of the VIVO source code distribution. -

-

Release anouncement for V1.2

-

- Text from the wiki page -

-

Upgrade process for V1.2

-

- -
    -
  1. - Before Performing the Upgrade -
    2. -
  2. - The Upgrade Process -
    3. -
  3. - Ontology Upgrade -
    4. -
      -
    1. - Verify Ontology upgrade process -
      2. -
    2. - Ontology knowledge base manual review -
      3. -
    -
  4. - Theme Modifications -
    5. -
- -

I. Before Performing the Upgrade

-

- Please ensure that backups are created of the: -

- -

- The upgrade process is similar to the original install process with the following - EXCEPTIONS: -

- -

The Upgrade Process

-
    -
  1. - Download the new distribution file and unpack it into a new source - directory. -
    2. -
  2. - Create deploy.properties, using the same values as in your previous - installation and set values for the new variables. -
    3. -
  3. - 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.
      • -
    • - NIH-funded VIVO Implmentations will need 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. -
      • -
    • - If you had used the vivo/contrib/FLShibboleth code in your previous release, - you should stop using it. Consult install.html or VIVO Release 1 v1.2 Installation Guide - on "Using an External Authentication System with VIVO". -
      • -
    -
    -
    4. -
  4. - If you had modified - - web.xml - - to configure the Pellet Reasoner (as described - in the installation instructions), repeat that modification. -
    5. -
  5. - Stop Apache Tomcat and run ant by typing: - - ant all - -
    6. -
  6. - Start Apache Tomcat and log in to VIVO. -
    7. -
- 
-
-
--------------------------------------------------------------------------------
-
-III. Ontology Changes
-
-A. Verify Ontology upgrade process
-
-After Apache Tomcat is started, these files should be reviewed to verify that
-the automated upgrade process was executed successfully.  The ontology alignment 
-process will create the following files in the Tomcat webapps/vivo/WEB-INF directory:
-
-ontologies/update/logs/knowledgeBaseUpdate.log 
-    A log of a summary of updates that were made to the knowledge base and notes 
-    about some recommended manual reviews. This file should end with
-    "Successfully finished processing ontology changes".
-    
-ontologies/update/logs/knowledgeBaseUpdate.error.log 
-    A log of errors that were encountered during the upgrade process. This file
-    should be empty if the upgrade was successful.
-    
-ontologies/update/changedData/removedData.n3
-    An N3 file containing all the statements that were removed from the knowledge base.
-    
-ontologies/update/changedData/addedData.n3
-    An N3 file containing all the statements that were added to the knowledge base.
-
-B. Ontology knowledge base manual review
-
-Changes to the VIVO core ontology may require corresponding
-modifications of the knowledge base instance data and local ontology
-extensions.
-
-When Apache Tomcat starts up following the upgrade, it will initiate 
-a process to examine the knowledge base and apply necessary changes.
-Not all of the modifications that may be required can be automated,
-so manual review of the knowledge base is recommended after the
-automated upgrade process. The automated process will make only 
-the following types of changes:
-
-  Class or Property renaming
-    All references to the class (in the subject or object position) will
-    be updated to the new name. References to the property will be
-    updated to the new name.
-  
-  Class or Property deletion
-    All individuals in a deleted class will be removed.
-   
-    All statements using a deleted property will be changed
-    to use the nearest available superproperty. If there is no available
-    superproperty then the statement will be deleted from the
-    knowledge base. Note that all removed and added data
-    is recorded in the files in the changedData directory.
-    
-  Property addition
-    If a newly added property is the inverse of a previously
-    existing property, the inverse of any statements using the
-    pre-existing property will be asserted.
-
-  Annotation property default values
-    If a site has modified the value of a vitro annotation (such as
-    displayRankAnnot or displayLimitAnnot) so that it is
-    no longer using the default, then that setting will be left unchanged.
-    If a site is using the default value of a vitro annotation, and the
-    default has been changed in the new version of the ontology, then
-    the new default value will be propagated to the knowledge base.
-
--------------------------------------------------------------------------------
-
-IV. Theme Changes
-
-VIVO 1.1 introduces the first step in a transition from JavaServer Pages (JSPs)
-to the FreeMarker template engine for generating web pages. As part of this 
-process, the JSP files that were used for theme customization in earlier 
-versions of VIVO have been replaced by a set of FreeMarker templates. 
-In the 1.1 install package, these files are located in 
-/vivo/themes/vivo-basic/templates and have an ftl (for FreeMarker Template
-Language) extension.
-
-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 1.0, follow the steps below
-under sections "Templates," "Stylesheets,"  and "Site Icons" to upgrade your 
-theme to VIVO 1.1.
-
-    1. Templates
-
-       a. Copy the directory /vivo/themes/vivo-basic/templates into your theme
-          directory /vivo/themes/.
-
-       b. Follow step i or ii below, whichever is applicable to your theme. 
-
-           i. If you did not apply any customizations to the JSPs in your VIVO  
-              1.0 theme, then you do not need to apply any additional changes 
-              to the VIVO 1.1 theme templates during the upgrade process.
-
-           ii. If you did apply customizations to the JSPs in your VIVO 1.0  
-               theme,you will need to hand-replicate those modifications in the 
-               new theme template files. 
-           
-               The theme template content that was previously contained in 
-               three JSP files is now contained in five FTL files. The 
-               correspondence between the 1.0 JSPs and the 1.1 FTLs is as 
-               follows:
-               
-                   identity.jsp => identity.ftl
-                   menu.jsp => menu.ftl and search.ftl
-                   footer.jsp => footer.ftl and googleAnalytics.ftl
-    
-               googleAnalytics.ftl is a new file to which you will add
-               your site's Google Analytics Tracking Code (see section II).
-           
-               Because the FreeMarker Template Language uses many syntactic 
-               conventions that will be familiar to template authors from JSP 
-               or other common templating systems, the translation of your JSP 
-               changes into the new FTLs should be relatively straightforward. 
-   
-               Consult the FreeMarker Template Author's Guide at 
-               http://freemarker.org/docs/dgui.html and the Reference at 
-               http://freemarker.org/docs/ref.html for complete documentation  
-               of the syntax and available built-in constructs. Template 
-               authors need  not be concerned with the Programmer's Guide or 
-               Java API documentation.
-
-       c. Remove the jsp directory from your themes directory.
-    
-    2. Stylesheets
-        
-       VIVO 1.1 includes changes to vivo-basic stylesheets. If you modified 
-       styles in your VIVO 1.0 theme, you will not be able to simply copy the  
-       1.0 stylesheets into your 1.1 theme, because you will then lose 1.1 
-       style upgrades that your theme should pick up.  Instead, you should 
-       use the vivo-basic 1.1 stylesheets as a starting point, and manually
-       merge your 1.0 style modifications in as needed.
-    
-    3. Site Icons
-    
-       Copy the site icons from your 1.0 theme into the site_icons folder in
-       your 1.1 theme.		
-		
-		
-		
-		
-		
-
-
- - - -