vivo/doc/upgrade-1.1.txt

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Upgrading NIH 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 NIH 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 Changes
IV.  File Storage 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 will use the password 
    previously set, NOT the password in deploy.properties.
* 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 uploads 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 changes you have made to the new source directory.

   Note: 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.

  >>>>>> TBD -- Note on Google Analytics Tracking code to footer.jsp? (lines 68-73 in update-1.0.txt)      
      
   Note: This process assumes any changes made to the application were made in 
      the source directory and deployed, and were not made directly within 
      Apache Tomcat webapp.
      
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 deploy by typing: ant deploy

7. If you have setup 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 login to VIVO.

9. Rebuild the Lucene search index as described in step IX of
the install process. This step will ensure that changes in the RDF
data to align with the latest version of the core ontology
will be reflected in the search index.

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III. Ontology Changes

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
    It 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.
  
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.

    
After Apache Tomcat is started, these files should be reviewed to verify that
the automated upgrade process was executed successfully.


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IV. 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.
    
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.

If, for any reason, the File Storage upgrade process is not successful,
VIVO will not start. Attempts to open VIVO in the browser will result in a
404 error. Tomcat's "localhost" log file will contain an exception listing
with more information.

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.