vivo/doc/upgrade-1.1.txt

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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.

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I.   Before Performing the Upgrade
II.  The Upgrade Process
III. Ontology Upgrade
     A. Verify Ontology upgrade process
     B. Ontology knowledge base manual r
IV.  New File Storage System
     A. Verifying the File Storage upgrade
     B. File Storage changes
V.   Theme Changes

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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 or reconfigure the Apache HTTP Server.
* 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 Changes"
    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.
         
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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 path=""
		docBase="/usr/local/tomcat/webapps/vivo"
		reloadable="true"
		cookies="true" >
		<Environment type="java.lang.String" override="false" 
			name="path.configuration" 
			value="deploy.properties"
		/>
	</Context>
	
	Context section after:
	
	<Context path=""
		docBase="/usr/local/tomcat/webapps/vivo"
		reloadable="true"
		cookies="true" >
		<Manager pathname="" />
		<Environment type="java.lang.String" override="false" 
			name="path.configuration" 
			value="deploy.properties"
		/>
	</Context>
	
8. Start "Apache Tomcat" and log in to VIVO.

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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 changed to
    belong to the nearest available superclass (which may be owl:Thing).
   
    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.
    
  Class or Property addition
    If a newly added class has a superclass and there are
    individuals in that superclass, then a note will be
    added to the log file suggesting review of those individuals to
    see if they should be reasserted in the newly added class.
  
    If a newly added property has a superproperty and there are
    statements using the superproperty, then a note will be added to
    the log file suggesting review of those statements to see if they
    should be reasserted using the newly added property.

  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.

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IV. New File Storage System

A. Verifying the File Storage upgrade

If the File Storage upgrade process is not successful, Tomcat's "vivo.all.log" 
log file will contain an exception listing with more information.

The File Storage upgrade process will create these files in the VIVO upload
directory:

upgrade/upgradeLog.2010-00-00T00-00-00.txt
    A log of the upgrade process. The actual filename includes a timestamp 
    that tells when the upgrade executed. This file should be inspected 
    for warnings or errors. The file should end with "File Storage update 
    is complete." 
    
upgrade/translatedImages
    Contains the images that were translated to the new file storage system.
    
upgrade/unreferencedImages
    Contains the images which were in the "images" directory, but were no
    longer referred to by any Individual. 
    
file_storage_root 
    A directory where the uploaded images are stored. Within the root, the
    path to the image is derived from its unique ID and its filename. 

file_storage_namespaces.properties
    Contains the URL prefix used when serving the image files.

B. File Storage changes

Changes to the File Storage system in VIVO result in new properties to describe
the relationships involving files, and a new directory structure in which to 
store the files.

Uploaded files are stored in the VIVO upload directory, as defined in the
deploy.properties file. Previously, images were stored in the "images" folder 
of the upload directory. Now, all uploaded files will be stored in the 
"file_storage_root" folder of the upload directory.

Previously, image files were served from the images directory within the web 
application, within Tomcat, and copied to the upload directory for backup 
purposes. Now, image files are stored only in the upload directory, and served
directly from there. The image directory within the web application is no 
longer used.

When Apache Tomcat starts up following the upgrade, it will initiate a process
which makes the required changes:

  Initializing the file storage system
    Each file will now be assigned a unique ID, in addition to its filename.
    Both the ID and filename are used to store the file within the system.
    Uploading two images with identical filenames will not cause a conflict.

  Pruning dead image references
    Previous versions allowed manual editing of file paths, sometimes resulting
    in erroneous information. Any image properties that refer to non-existent
    files will be removed.
    
  Removing unreferenced images
    Any uploaded image which is no longer referred to by an Individual will
    be removed.
    
  Generating main images and/or thumbnails
    Each image will be represented by both a main image file and a 
    thumbnail image file. If either of these is missing for a particular 
    individual, it will be created.  
    
  Converting image properties on Individuals
    Image properties previously were simple data properties, referring to 
    the filename and path. These are replaced by object properties, which
    refer to the file by its unique ID.
    
  Translating images into the new directory structure
    Each image file will be copied to its new location in the upload
    directory.
  
  Cleaning the old image directory
    All image files are removed from their old locations in the upload 
    directory.

Once you are satisfied that the File Storage upgrade process is successful,
you may delete the "images" folder and the "upgrade" folder from the upload 
directory. You may also delete the WEB-INF/images directory from within
your Tomcat web application. 

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V. 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/<your-theme-name>.

       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.