NIHVIVO-2936 upgrade-1.3.html
Added in text for release announcement that Jon edited. Added print border for deploy.properties. Fixed typos found by Tim.
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<div id="wrapper-content" role="main">
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<h1>VIVO Release 1 v1.3 Upgrade Guide</h1>
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<small>
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July 22, 2011 - Upgrading from Release 1 v1.2 to Release 1
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v1.3
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July 22, 2011 - Upgrading from Release 1 v1.2 to Release 1 v1.3
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</small>
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<toc>
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<ul>
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@ -43,12 +42,99 @@
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or software requirements for V1.3).
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</p>
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<h3 id="announcement">Release Announcement for V1.3</h3>
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<p>
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https://confluence.cornell.edu/x/3B4DCQ - get content from the wiki
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page before final release.
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V<!-- Release Announcement -->IVO Release 1.3 incorporates changes to
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the search indexing, user
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accounts, menu management, ontology, and visualizations.
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<br>
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</p>
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<!-- Release Announcement --><hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.3</h2>
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<h4>Search</h4>
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VIVO 1.3 will feature notable improvements to the local search,
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primarily to improve relevance ranking but also to boost the influence
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of semantic relationships in the search. This will improve recall by
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including text from related resources (e.g., adding a person’s grant
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and publication titles to his or her search entry) and by boosting
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overall relevance ranking based on the number and nature of connections
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from one individual to others.
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<br>
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VIVO is now using Apache Solr (http://lucene.apache.org/solr/) in place
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of Apache Lucene to improve indexing and faceting of search results.
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The migration to Solr also aligns the local search with the VIVO
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multi-site search site under development for release prior to the 2011
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VIVO Conference.
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<br>
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<h4>Authorization</h4>
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Release 1.3 provides an entirely new model of authorization within the
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VIVO application to allow more granular control over system
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configuration and editing. The first phase of the new user account
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interface is included in V1.3. This interface provides a user search, a
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root acount, and password reset functionality where the password gets
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emailed to the user. The next phase will provide the ability to create
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new roles.
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<br>
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<h4>Menu management</h4>
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The menus across the top of the site (Home, People, Organizations,
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Research, Events) can now be managed in a web form instead of editing
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an RDF file. In addition to making site management much easier,
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form-based editing also allows more control over what classes of data
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are displayed and provides a mechanism to limit certain menu pages to
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content identified as internal to the institution.
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<br>
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<h4>FreeMaker template improvements</h4>
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While less directly visible to the public, version 1.3 also includes
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additional changes focused directly on supporting open source community
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involvement in extending and customizing VIVO. The development team
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began a year ago to transition VIVO’s code base away from Java Server
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Pages to the FreeMarker page templating system that much more cleanly
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separates internal application programming logic from page display.
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<br>
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<h4>Visualization</h4>
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The visualization team has implemented a Science Map visualization,
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which allows users to visually explore the scientific strengths of a
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university, school, department, or person in the VIVO instance. Users
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will be able to see where an organization or person’s interests lay
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across 13 major scientific disciplines or 554 sub-disciplines, and will
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be able to see how these disciplines and sub-disciplines interrelate
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with one another on the map of science. Wireframes and design
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documentation for upcoming enhanced versions of the Science Map
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visualization have already been developed; the Science Map
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visualization will most likely be in the form of a PDF that a user can
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download.
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<br>
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Several visualization also now provide a caching feature that improves
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performance after the initial processing.
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<br>
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<h4>QR Codes</h4>
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Pages for people in VIVO have the option of displaying QR codes.
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<br>
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<h4>Ontology changes</h4>
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<ul>
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<li>
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support for certifications and licenses
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</li>
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<li>
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expanded support for intellectual property (patents) (it was
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there as stub before but didn't allow common things such as assignee
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and issuer)
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</li>
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<li>
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support for editorial, reviewing and organizing activities
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</li>
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<li>
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expanded shared geographical instance data vocabulary to include
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the 50 U.S. states
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</li>
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<li>
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representing specific types of EducationalTraining:
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PostdoctoralTraining, Internship, MedicalResidency
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</li>
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</ul>
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<h4>Linked open data</h4>
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Responses to linked data requests have been enhanced to include
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additional context about any individual, in working toward a goal of
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being able to provide all the data in a person's profile available as
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RDF via a single web request.
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<br>
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<br>
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<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.3</h2>
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<toc>
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<ol class="roman1">
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<li>
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@ -92,14 +178,10 @@
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</li>
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<li>
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<a href="#root_account">Each VIVO installation will have a
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“root” account</a>
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'root' account</a>
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</li>
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</ol>
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</li>
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<li>
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<a href="#setup_sdb">Set Up SDB Store in the Background
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(Optional)</a>
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</li>
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</ol>
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</toc>
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<h3 id="preparation">I. Before Performing the Upgrade</h3>
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@ -123,8 +205,8 @@
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</p>
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<ul>
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<li>
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If you are still in RDB mode, it is required that you
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move your triple store to SDB while still at V1.2 (see <a href="ejc12_upgrade-1.3.html#triple_store">Triple Store</a>
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If you are still in RDB mode, it is required that you move your
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triple store to SDB while still at V1.2 (see <a href="ejc12_upgrade-1.3.html#triple_store">Triple Store</a>
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info
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below).
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<br>
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@ -144,7 +226,8 @@
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First-time login of the administrator account after the upgrade
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process is complete will use the password previously set, NOT the
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default password used on the first login after the initial
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installation.
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installation. With V1.3 there is also a new root user. Please see the
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section on <a href="#authorization">Authorization changes</a> for more information.
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</li>
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<li>
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The first time Apache Tomcat starts up after the upgrade, it
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VIVO 1.3 now requires you to use Jena's SPARQL database (SDB) for
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the triple store technology. Jena's legacy relational database
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store (RDB) was used by VIVO 1.1.1 and earlier. Both SDB and RDB
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were available in VIVO 1.2 and 1.2.1. It is required that
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you move your triple store to SDB while still at V1.2.
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were available in VIVO 1.2 and 1.2.1. It is required that you
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move your triple store to SDB while still at V1.2.
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</p>
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<p>
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SDB mode caches only a fraction of the RDF data in memory. Most
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queries are issued directly against the underlying database. This
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allows VIVO installations to display data from large RDF models while
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requiring only a small amount of server memory to run the application.
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There is a tradeoff in response time: pages make take slightly longer
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There is a tradeoff in response time: pages may take slightly longer
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to load in SDB mode, and performance will depend on the configuration
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parameters of the database server. Additionally, advanced OWL reasoning
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(not enabled by default in either mode) is not possible in SDB mode.
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</p>
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<p>
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A conversion from RDB to SDB mode can take a number of hours to
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complete if the
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installation contains a large amount of RDF data (roughly a million
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triples or more). You can start the conversion process in the
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background
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while the RDB system is running. This will reduce the delay in initial
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startup after the application is redeployed with deploy.properties set
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for SDB. <span style="font-weight: bold;">Note that it is important
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not to edit any data anywhere in the
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application while this background conversion is running</span>.
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complete if the installation contains a large amount of RDF data
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(roughly a million triples or more). You can start the conversion
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process in the background while the RDB system is running. This will
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reduce the delay in initial startup after the application is redeployed
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with deploy.properties set for SDB. <span style="font-weight: bold;">Note
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that
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it is important not to edit any data anywhere in the application
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while this background conversion is running</span>.
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</p>
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<p>
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To start the SDB conversion, log in as a system administrator and
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2. Create a new deploy.properties using the same values as in your
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previous installation and set values for the new variables as described
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below (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
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vitro.home.directory,
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email.smptHost, email.replyTo, rootUser.emailAddress)
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vitro.home.directory, email.smptHost, email.replyTo,
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rootUser.emailAddress)
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<br>
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</p>
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<p>
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<!-- deploy.properties table from install.html -->
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</p>
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<table>
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<table border='1' bordercolor="#CCCCCC" cellspacing="5">
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<tbody>
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<tr>
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<th>
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@ -650,9 +732,7 @@
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implementation sites and a copy of your institution's tracking code,
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see the <a href="https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI">VIVO
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Google
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Analytics
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wiki
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page</a>.
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Analytics wiki page</a>.
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</li>
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<li>
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If you had used the <code>vivo/contrib/FLShibboleth</code>
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@ -671,7 +751,7 @@
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that modification.
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</p>
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<p>
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5. Stop Apache Tomcat and run ant by typing: <code>ant all</code>
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5. Stop Apache Tomcat and from your VIVO source directory, run ant by typing: <code>ant all</code>
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</p>
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<p>
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6. Start Apache Tomcat and log in to VIVO.
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@ -790,14 +870,14 @@
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<ul>
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<li>
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<p>
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The <code>${stylesheets}</code>, <code>${scripts}</code>, and <code>${headScripts}</code>
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The <code>${stylesheets}</code>, <code>${scripts}</code>, and<code>${headScripts}</code>
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<code>add()</code>
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methods now
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take the full tag as an argument. This will require a change to all
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calls to these methods in the templates. This change allows for
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specification of attributes such as <code>media</code>
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directly
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in the tag. For example:
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methods now take
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the full tag as an argument. This will require a change to all calls to
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these methods in the templates. This change allows for specification of
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attributes such as <code>media</code>
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directly in the tag. For
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example:
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</p>
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<blockquote>
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1.2: <code>${stylesheets.add("/css/individual/individual.css")}</code>
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<p>
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Note the inclusion of <code>${urls.base}</code>
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in the 1.3
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example.
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The <code>add()</code>
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method no longer prefixes the context path to
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the url, so the full
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url must be specified in the tag.
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example. The <code>add()</code>
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method no longer prefixes the context
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path to the url, so the full url must be specified in the tag.
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</p>
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</li>
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<li>
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The <code>addFromTheme()</code>
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methods of the <code>${stylesheets}</code>,<code>${scripts}</code>, and<code>${headScripts}</code>
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objects have been deleted. Substitute
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as shown in the
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preceding example.
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methods of the <code>${stylesheets}</code>,<code>${scripts}</code>,
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and<code>${headScripts}</code>
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objects have been deleted. Substitute as
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shown in the preceding example.
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</li>
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<li>
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<code>propertyGroups.getPropertyAndRemoveFromList()</code>
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in the
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individual templates has been deprecated. The replacement method is <code>propertyGroups.pullProperty()</code>.
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There is no change in functionality.
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in
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the individual templates has been deprecated. The replacement method is<code>propertyGroups.pullProperty()</code>. There is no change in
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functionality.
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</li>
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</ul>
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<h3 id="listview">VI. List view changes</h3>
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<code><query-base></code>
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and <code><query-collated></code>
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have been replaced
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with a single query <code><query-select></code>
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that contains
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tags for
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fragments to be used only in the collated version of the query. This
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and other changes are documented in <code>/vitro/doc/list_view_configuration_guidelines.txt</code>.<h3 id="authorization">VII. Authorization changes</h3>
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have been replaced with a single query <code><query-select></code>
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that contains tags for fragments to be used only in the collated
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version of the query. This and other changes are documented in <code>/vitro/doc/list_view_configuration_guidelines.txt</code>.<h3 id="authorization">VII. Authorization changes</h3>
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<p>
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In release 1.3, the VIVO authorization system has some extensive
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changes. In summary, these are:
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<p>
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Prior to release 1.3, each user account was identified by a
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Username field. This field was labeled as “E-mail address” on some
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pages in VIVO, but so mail was ever sent. In release 1.3, this has
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pages in VIVO, but no mail was ever sent. In release 1.3, this has
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changed, so the e-mail address is fully used, both for identification
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and for communication with the user.
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</p>
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<dd>
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<p>
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Prior to release 1.3, the Username field (also referred to as
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“e-mail address”) was used for several purposes:
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'e-mail address') was used for several purposes:
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</p>
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<ul>
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<li>
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@ -914,7 +989,8 @@
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</p>
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<ul>
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<li>
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EmailAddress is used when logging in (along with a password).
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EmailAddress is used when logging in (along with a
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password).
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</li>
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<li>
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EmailAddress is used to send notifications to the user about
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<p>
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When creating a new user account, or editing an existing one,
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the system requires that your e-mail address be in a valid form, like <code>somebody@somewhere.edu</code>.
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You should plan for this as part of your migration to release 1.3
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You
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should plan for this as part of your migration to release 1.3
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</p>
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</dd>
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</dl>
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@ -1003,9 +1080,9 @@
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<dd>
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<p>
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The e-mail notification relies on two configuration properties:<code>email.smtpHost</code>
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and <code>email.replyTo</code>. If
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either of these properties is missing or empty, VIVO will not attempt
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to send e-mail notifications to users.
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and <code>email.replyTo</code>. If either of these properties is
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missing or empty, VIVO will not attempt to send e-mail notifications to
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users.
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</p>
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<p>
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This can be useful for small or experimental installations of
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@ -1019,7 +1096,7 @@
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</p>
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</dd>
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</dl>
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<h4 id="root_account">iii. Each VIVO installation will have a “root”
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<h4 id="root_account">iii. Each VIVO installation will have a 'root'
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account.</h4>
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<dl>
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<dd>
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@ -1034,7 +1111,8 @@
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</p>
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<pre>rootUser.emailAddress = vivo_root@mydomain.edu</pre>
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The password for this account is automatically set to <code>rootPassword</code>,
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but you will be required to change the password the first time you log
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but
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you will be required to change the password the first time you log
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in.
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<blockquote>
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<strong>Note:</strong>
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