NIHVIVO-511 start the 1.1 upgrade document.
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doc/upgrade-1.1.txt
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-------------------------------------------------------------------------------
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Upgrading NIH VIVO
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Steps to Upgrade from Release 1 Version 1.0 to Release 1 Version 1.1
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This file provides a short description of the steps involved in upgrading your
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installation of NIH VIVO from Release 1 Version 1.0 to Release 1 Version 1.1.
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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 Changes
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IV. File Storage 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 or reconfigure 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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* 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 Changes"
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below for more information.
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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 uploads directory (images), to align
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the uploaded files with the revised file storage scheme. See the section
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on "File Storage Changes" 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 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 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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>>>>>> TBD -- Note on Google Analytics Tracking code to footer.jsp? (lines 68-73 in update-1.0.txt)
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Note: 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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Apache Tomcat webapp.
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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 deploy by typing: ant deploy
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7. If you have setup the Apache Tomcat Connector using mod_jk and modified your
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tomcat/conf/server.xml file, you will need to add a line to your context
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section specifying a "Manager" tag; see examples below.
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Context section before:
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<Context path=""
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docBase="/usr/local/tomcat/webapps/vivo"
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reloadable="true"
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cookies="true" >
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<Environment type="java.lang.String" override="false"
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name="path.configuration"
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value="deploy.properties"
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/>
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</Context>
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Context section after:
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<Context path=""
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docBase="/usr/local/tomcat/webapps/vivo"
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reloadable="true"
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cookies="true" >
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<Manager pathname="" />
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<Environment type="java.lang.String" override="false"
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name="path.configuration"
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value="deploy.properties"
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/>
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</Context>
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8. Start "Apache Tomcat" and login to VIVO.
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9. Rebuild the Lucene search index as described in step IX of
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the install process. This step will ensure that changes in the RDF
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data to align with the latest version of the core ontology
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will be reflected in the search index.
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-------------------------------------------------------------------------------
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III. Ontology Changes
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>>>>>> TBD
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-------------------------------------------------------------------------------
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IV. File Storage Changes
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Changes to the File Storage system in VIVO result in new properties to describe
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the relationships involving files, and a new directory structure in which to
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store the files.
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Uploaded files are stored in the VIVO upload directory, as defined in the
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deploy.properties file. Previously, images were stored in the "images" folder
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of the upload directory. Now, all uploaded files will be stored in the
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"file_storage_root" folder of the upload directory.
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Previously, image files were served from the images directory within the web
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application, within Tomcat, and copied to the upload directory for backup
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purposes. Now, image files are stored only in the upload directory, and served
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directly from there. The image directory within the web application is no
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longer used.
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When Apache Tomcat starts up following the upgrade, it will initiate a process
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which makes the required changes:
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Initializing the file storage system
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Each file will now be assigned a unique ID, in addition to its filename.
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Both the ID and filename are used to store the file within the system.
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Uploading two images with identical filenames will not cause a conflict.
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Pruning dead image references
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Previous versions allowed manual editing of file paths, sometimes resulting
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in erroneous information. Any image properties that refer to non-existent
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files will be removed.
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Removing unreferenced images
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Any uploaded image which is no longer referred to by an Individual will
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be removed.
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Generating main images and/or thumbnails
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Each image will be represented by both a main image file and a
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thumbnail image file. If either of these is missing for a particular
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individual, it will be created.
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Converting image properties on Individuals
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Image properties previously were simple data properties, referring to
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the filename and path. These are replaced by object properties, which
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refer to the file by its unique ID.
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Translating images into the new directory structure
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Each image file will be copied to its new location in the upload
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directory.
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Cleaning the old image directory.
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All image files are removed from their old locations in the upload
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directory.
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The File Storage upgrade process will create these files in the Vivo upload
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directory:
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upgrade/upgradeLog.2010-00-00T00-00-00.txt
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A log of the upgrade process. The actual filename includes a timestamp
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that tells when the upgrade executed. This file should be inspected
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for warnings or errors. The file should end with "File Storage update
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is complete."
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upgrade/translatedImages
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Contains the images that were translated to the new file storage system.
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upgrade/unreferencedImages
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Contains the images which were in the "images" directory, but were no
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longer referred to by any Individual.
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file_storage_root
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A directory where the uploaded images are stored. Within the root, the
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path to the image is derived from its unique ID and its filename.
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file_storage_namespaces.properties
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Contains the URL prefix used when serving the image files.
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If, for any reason, the File Storage upgrade process is not successful,
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VIVO will not start. Attempts to open VIVO in the browser will result in a
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404 error. Tomcat's "localhost" log file will contain an exception listing
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with more information.
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Once you are satisfied that the File Storage upgrade process is successful,
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you may delete the "images" folder and the "upgrade" folder from the upload
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directory. You may also delete the WEB-INF/images directory from within
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your Tomcat web application.
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