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< h1 > VIVO Release 1 V1.5 Upgrade Guide< / h1 >
< small >
February 15, 2012 - Upgrading from Release 1 V1.4 to Release 1 V1.5
< / small >
< p >
This document contains instructions on how to upgrade your
installation of VIVO from Version 1.4 (or 1.4.1) to Version 1.5.
This and other documentation can be found on the < a href = "http://vivoweb.org/support" > support page< / a >
at < a href = "http://vivoweb.org/" > VIVOweb.org< / a >
< / p >
< p >
If you need to do a fresh install, please consult the VIVO Release V1.5 Installation
Guide found on < a href = "http://vivoweb.org/support" > vivoweb.org< / a >
or the install.html file located in the < code > doc< / code >
directory of the VIVO source code distribution. The installation document also has a
list of the required software and versions.
< / p >
< p >
For a description of the release contents see the < a href = "./release.html" > Release announcement for V1.5< / a > .
< / p >
< hr / >
< h3 id = "tableofcontents" > Table of Contents< / h3 >
< toc >
< ol class = "roman2" >
< li > < a href = "#preparation" > Before Performing the Upgrade< / a > < / li >
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< li >
< a href = "#changes" > Noteworthy Changes< / a >
< ol class = "roman2" >
< li > < a href = "#upgradeAnt" > Ant version 1.8 is required< / a > < / li >
< li > < a href = "#customShortView" > Custom short views< / a > < / li >
< li > < a href = "#openSocial" > Support for OpenSocial gadgets< / a > < / li >
< li > < a href = "#browsers" > Supported Browsers< / a > < / li >
< / ol >
< / li >
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< li > < a href = "#upgrade_process" > Upgrade Instructions< / a > < / li >
< li > < a href = "#kbm" > Knowledge Base Migration< / a > < / li >
< li > < a href = "#termsofuse" > Review the VIVO Terms of Use< / a > < / li >
< li > < a href = "#nextsteps" > Next Steps< / a > < / li >
< / ol >
< / toc >
< hr / >
< h3 id = "preparation" > I. Before Performing the Upgrade< / h3 >
< br / >
Create backups of:
< ul style = "list-style-type: square;" >
< li >
The VIVO distribution directory (which contains the source for VIVO 1.4 or VIVO 1.4.1)
< / li >
< li >
The VIVO home directory (pointed to by your deploy.properties file)
< / li >
< li >
The webapps directory in Tomcat
< / li >
< li >
MySQL database (most people use mysqldump to create the backup)
< / li >
< / ul >
< p >
The upgrade process is similar to the initial install process
with
the following exceptions:
< / p >
< ul >
< li >
You do not need to reinstall MySQL or recreate the MySQL database. Please
backup your MySQL database as noted above.
< / li >
< li >
First-time login of the root 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.)
< / li >
< li >
The first time Apache Tomcat starts up after the upgrade, an automated
process will modify the knowledge base to align the
data with any ontology updates made for the new release. See the section on the < a href = "#kbm" > Knowledge Base Migration< / a >
below for more information.
< / li >
< / ul >
< h3 id = "changes" > II. Noteworthy Changes< / h3 >
< ul >
< li >
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< h4 id = "upgradeAnt" > Ant version 1.8 is required< / h4 >
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< p >
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The VIVO build script has been revised, and now requires features from
version 1.8 of Apache Ant. Version 1.8 has been available since February, 2010.
The current version of Apache Ant is 1.8.4.
< / p >
< p >
You can find recent versions of Apache Ant at
< a href = "http://ant.apache.org" > http://ant.apache.org< / a >
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< / p >
< / li >
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< li >
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< h4 id = "customSearchView" > Custom short views< / h4 >
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< p >
"Custom search views" have been re-implemented as part of the more flexible "Custom short views" mechanism.
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If you have implemented custom search views, you will need to re-configure them to fit the new framework.
For an explanation of how to use custom search views, consult the
< a href = "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Using_Short_Views_in_Release_1.5" >
SourceForge Wiki page on custom search views
< / a >
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< / p >
< / li >
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< li >
< h4 id = "openSocial" > Support for OpenSocial gadgets< / h4 >
< p >
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VIVO can now be configured to support Open Research Networking Gadgets,
an extension of OpenSocial gadgets. For a description of this, and instructions
for configuring VIVO, look at < a href = "./setting_up_orng.html" > setting_up_orng.html< / a > , in this directory.
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< / p >
< / li >
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< li >
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< h4 id = "browsers" > Supported Browsers< / h4 >
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< p >
For this release, the following browsers are supported.
< / p >
< p >
Mac:
< / p >
< ul >
< li > Chrome 8.0.552.237< / li >
< li > FireFox 3.6.13< / li >
< li > Opera 10.6.2< / li >
< li > Safari 5.0.3< / li >
< / ul >
< p >
PC:
< / p >
< ul >
< li > Chrome 8.0.552.273< / li >
< li > FireFox 10.0.2< / li >
< li > Internet Explorer 7, 8, 9< / li >
< li > Opera 10.6.2< / li >
< / ul >
< / li >
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< / ul >
< h3 id = "#upgrade_process" > III. Upgrade Instructions< / h3 >
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< p >
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1. Download the new distribution file and unpack it into a new
source directory.
< / p >
< p >
2. Create a new deploy.properties using the same settings as in
your previous installation and set values for the new variables as described
below:
< br >
< / p >
< p >
<!-- deploy.properties table from install.html -->
< / p >
< table border = '1' bordercolor = "#CCCCCC" cellspacing = "5" >
< tbody >
< tr >
< th >
Property Name
< / th >
< th >
Example Value
< / th >
< / tr >
< tr >
< td colspan = "2" >
Show only the most appropriate data values based on the Accept-Language
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header supplied by the browser. Default is false if not set.
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< / td >
< / tr >
< tr class = "odd_row blue" >
< td >
RDFService.languageFilter
< / td >
< td >
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false
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< / td >
< / tr >
< tr >
< td colspan = "2" >
These values are used when deploying VIVO as an OpenSocial container
and integrating with OpenSocial gadgets.
For instructions, look at < a href = "./setting_up_orng.html" > setting_up_orng.html< / a > , in this directory.
If you are creating
a VIVO installation that does not use OpenSocial gadgets, these values are omitted.
< / td >
< / tr >
< tr class = "odd_row blue" >
< td >
OpenSocial.shindigURL< br >
OpenSocial.tokenService< br >
OpenSocial.tokenKeyFile< br >
OpenSocial.sandbox
< / td >
< td >
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< / tr >
< / tbody >
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< p >
3. Apply any previous changes you have made to the new source
directory.
< / p >
< blockquote >
< strong > Special notes regarding source files< / strong >
< ul >
< li >
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.
< / li >
< li >
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.
< / li >
< li >
NIH-funded VIVO implementations will need to apply the
Google
Analytics Tracking Code (GATC) to < code > googleAnalytics.ftl< / code >
in
the theme:< pre > [new_source_directory]/themes/[theme_dir]/templates/googleAnalytics.ftl< / pre >
A sample < code > googleAnalytics.ftl< / code >
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 of your institution's tracking code,
see the < a href = "https://confluence.cornell.edu/display/ennsrd/Google+Analytics+for+UI" > VIVO
Google
Analytics
wiki
page< / a > .
< / li >
< / ul >
< / blockquote >
< p >
5. Stop Apache Tomcat and from your VIVO source directory, run
ant
by typing: < code > ant all< / code >
< / p >
< p >
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.< pre > INFO: Server startup in XXXXX ms< / pre >
< / p >
< p >
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".
< / p >
< p >
8. Review and save aside the knowledge base migration logs.
The knowledge base migration process described in the next section will generate logs.
These logs will be overwritten if you redeploy the VIVO application (but not if you restart tomcat), and since
they may be a useful reference if questions come up about your 1.5 VIVO data after deployment,
you should save them aside.
The logs are created in the Tomcat < code > webapps/vivo/WEB-INF directory< / code > :
< / p >
< dl >
< dt >
< code > ontologies/update/logs/knowledgeBaseUpdate.(timestamp).log< / code >
< / dt >
< dd >
A log of a summary of updates that were made to the knowledge
base. 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.
< / dd >
< / dl >
< dl >
< dt >
< code > ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log< / code >
< / dt >
< dd >
A log of errors that were encountered during the upgrade
process. This file should be empty if the upgrade was successful. If any errors are encountered
you will need to rerun the knowledge base migration.
< / dd >
< / dl >
< h3 id = "#kbm" > IV. Knowledge Base Migration< / h3 >
< p >
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Changes to the VIVO core ontology may require corresponding
modifications to the knowledge base instance data and ontology annotations.
When VIVO first starts up following the upgrade, it will
initiate a process to examine the knowledge base and apply necessary
changes. The knowledge base migration process for release 1.5 will make
the following types of changes:
< / p >
< dl >
< dt >
The vivo:ResearchLaboratory class has been removed. All instances of vivo:ResearchLaboratory will be
retyped to its superclass vivo:Laboratory.
< / dt >
< / dl >
< dl >
< dt >
Annotation property default values
< / dt >
< dd >
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.
< br >
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.
< / dd >
< / dl >
< p >
In addition to the logs described in < strong > step 8< / strong > of the < a href = "#upgrade_process" > previous section< / a > , the knowledge base migration
process will log copies of all additions and deletions that were made to the knowledge base in the following files:
< / p >
< dl >
< dt >
< code > webapps/vivo/WEB-INF/ontologies/update/changedData/removedData.n3< / code >
< / dt >
< dd >
An N3 file containing all the statements that were removed from the knowledge base.
< / dd >
< / dl >
< dl >
< dt >
< code > webapps/vivo/WEB-INF/ontologies/update/changedData/addedData.n3< / code >
< / dt >
< dd >
An N3 file containing all the statements that were added to the knowledge base.
< / dd >
< / dl >
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< h3 id = "termsofuse" > V. Review the VIVO Terms of Use< / h3 >
< p >
VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"
you assign in the "Site Information" form under the < strong > Site Admin< / strong >
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:< pre > [vivo_source_dir]/vitro-core/webapp/web/templates/freemarker/body/termsOfUse.ftl< / pre >
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.
< / p >
< h3 id = "nextsteps" > Next Steps< / h3 >
< p >
Now that you have VIVO up and running, please refer to the < a href = "http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide" > Site Administrator's Guide< / a >
for information about its operation.
< / p >
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