VIVO Release 1 V1.4 Upgrade Guide

- Upgrading from Release 1 V1.3 to Release 1 V1.4 + December 9, 2011 - Upgrading from Release 1 V1.3 to Release 1 V1.4 + + + +

+ This document provides a short description of the steps involved in + upgrading your installation of VIVO from Version 1.3 to Version 1.4. + This and other documentation can be found on the support page + at VIVOweb.org +

+

+ If you need to do a fresh install, please consult the VIVO Release V1.4 Installation + Guide found on vivoweb.org + or the install.html file located in the doc + directory of the VIVO source code distribution. The installation document also has a + list of the required software and versions (there are no new hardware + or software requirements for V1.4). +

+

Release Announcement for V1.4

+ +

TBD

+
+

Upgrade process for V1.4

+ +
    +
  1. + Before Performing the Upgrade +
    2. +
  2. + Noteworthy Changes +
    +
      +
    1. + Template changes +
      2. +
    2. + Profile editing by Proxies +
      3. +
    3. + Change to Tomcat configuration +
      4. +
    +
    3. +
  3. + The Upgrade Process +
    4. +
  4. + Ontology Changes +
      +
    1. + Verify + Ontology upgrade process +
      2. +
    2. + Ontology + knowledge + base + manual review +
      3. +
    +
    5. +
  5. + Review the VIVO Terms of Use +
    6. +
+ -

Template changes

- -

changes to the build script

- - -

Tomcat configuration

- + +

+ 4. If you had modified web.xml + to configure the + Pellet Reasoner (as described in the installation instructions), repeat + that modification. +

+

+ 5. Stop Apache Tomcat and from your VIVO source directory, run + ant + by typing: ant all +

+

+ 6. Start Apache Tomcat and log into VIVO as the root user when the upgrade is + completed. Depending on the size of your database, the migration process may + take up to several hours. When it is complete, you will + see a message in the catalina.log file that the server has started.

INFO: Server startup in XXXXX ms
+

+

+ 7. As root or an administrator, request a rebuild of the Solr search index: + Go to the "Site Admin" page and click on "Rebuild Search Index" under the + heading "Refresh Content". +

+

IV. Ontology Changes

+

i. 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.(timestamp).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 "Finished knowledge base migration". If this file contains any + warnings they should be reviewed with your implementation team + representative to see whether any corrective action needs to be taken. +
+
+
+
+ ontologies/update/logs/knowledgeBaseUpdate.(timestamp).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. +
+
+

ii. 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 type assertions of 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. +
+
+

V. Review the VIVO Terms of Use

+

+ VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name" + you assign in the "Site Information" form under the Site Admin + area will be + inserted into the "Terms of Use" statement. If you want to edit the text content more than just + the "Site Name", the file can be found here:

[vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl
+ Be sure to make the changes in your source files and deploy them to your tomcat so you don't lose + your changes next time you deploy for another reason. +

+

Next Step ...

+

+ Now that you have VIVO up and running, please go read the Site Administrator's Guide. +

+