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doc/upgrade-1.4.html
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@ -16,19 +16,9 @@
<small>
December 9, 2011 - Upgrading from Release 1 V1.3 to Release 1 V1.4
</small>
<toc>
<ul>
<li>
<a href="#announcement">Release announcement for V1.4</a>
</li>
<li>
<a href="#upgrade">Upgrade process for V1.4</a>
</li>
</ul>
</toc>
<p>
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 document contains instructions on how to upgrade your
installation of VIVO from Version 1.3 to Version 1.4.
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>
@ -40,108 +30,102 @@
list of the required software and versions (there are no new hardware
or software requirements for V1.4).
</p>
<h3 id="announcement">Release Announcement for V1.4</h3>
<!-- Release Announcement -->
<p><em>TBD</em></p>
<br>
<hr><!-- Page break --><!-- Upgrade process for V1.4 --><h2 id="upgrade">Upgrade process for V1.4</h2>
<p>
For a description of the release contents see the <a href="TODOaddLinkToAnnouncement">Release announcement for V1.4</a>.
</p>
<hr/>
<!-- Upgrade process for V1.4 --><h3 id="tableofcontents">Table of Contents</h3>
<toc>
<ol class="roman1">
<li>
<a href="#preparation">Before Performing the Upgrade</a>
</li>
<li>
<a href="#changes">Noteworthy Changes</a>
<a>Upgrade process for V1.4</a>
<br>
<ol class="roman2">
<li>
<a href="#template_changes">Template changes</a>
</li>
<li>
<a href="#proxy_editing">Profile editing by Proxies</a>
</li>
<li>
<a href="#tomcat_setup">Change to Tomcat configuration</a>
</li>
</ol>
</li>
<li>
<a href="#upgrade_process">The Upgrade Process</a>
</li>
<li>
<a href="#ontology">Ontology Changes</a>
<ol class="roman3">
<li>
<a href="#verify_ontology_upgrade">Verify
Ontology upgrade process</a>
</li>
<li>
<a href="#ontology_knowledge_base">Ontology
knowledge
base
manual review</a>
</li>
<ol class="roman2">
<li>
<a href="#preparation">Before Performing the Upgrade</a>
</li>
<li>
<a href="#changes">Noteworthy Changes</a>
<br>
<ol class="roman2">
<li>
<a href="#template_changes">Template changes</a>
</li>
<li>
<a href="#proxy_editing">Profile editing by Proxies</a>
</li>
<li>
<a href="#tomcat_setup">Change to Tomcat configuration</a>
</li>
</ol>
</li>
<li>
<a href="#upgrade_process">The Upgrade Process</a>
</li>
<li>
<a href="#kbm">Knowledge Base Migration</a>
<ol class="roman3">
<li>
<a href="#verifymigration">Knowledge Base Migration Process</a>
</li>
<li>
<a href="#reviewkbm">Knowledge Base Manual Review for Local Extensions</a>
</li>
</ol>
</li>
</ol>
</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>
<p>
Please ensure that backups are created of the:
</p>
<br/>
Create backups of the:
<ul style="list-style-type: square;">
<li>
Tomcat webapps directory
</li>
<li>
Original source directory
Original source directory (TODO: I think we should specifically name the directory (I don't know what's intended) sjm)
</li>
<li>
MySQL database (mysqldump)
</li>
</ul>
<p>
The upgrade process is similar to the original install process
The upgrade process is similar to the initial install process
with
the following EXCEPTIONS:
the following exceptions:
</p>
<ul>
<li>
If you are still in RDB mode, it is required that you move
your
triple store to SDB while still at V1.2 (see <a href="#triple_store">Triple
Store</a>
info below).&nbsp;
<br>
</li>
<li>
DO NOT reinstall MySQL or recreate the MySQL database. Please
ensure that you back-up the MySQL database.
</li>
<li>
It is not necessary to add RDF data.
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
process is complete will use the password previously set (not the
default password used on the first login after the initial
installation.
installation.)
</li>
<li>
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 the <a href="#ontology">Ontology Upgrade</a>
below for more information.
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="#ontology">Ontology Upgrade</a>
below for more information. Note that
</li>
</ul>
<h3 id="changes">II. Noteworthy Changes</h3>
<p>(TOTO: I think this should contain only changes to the upgrade process itself. Changes to the source code that are too detailed for the release announcement could go in
an appendix (final section) to this document until such time as there is an granual release changes document.</p>
<h4 id="template_changes">i. Template changes
</h4>
<ul>
@ -176,9 +160,8 @@
source directory.
</p>
<p>
2. Create a new deploy.properties using the same values as in
your
previous installation and set values for the new variables as described
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 (vitro.local.solr.url, vitro.local.solr.ipaddress.mask,
vitro.home.directory, email.smptHost, email.replyTo,
rootUser.emailAddress)
@ -649,12 +632,6 @@
</li>
</ul>
</blockquote>
<p>
4. If you had modified <code>web.xml</code>
to configure the
Pellet Reasoner (as described in the installation instructions), repeat
that modification.
</p>
<p>
5. Stop Apache Tomcat and from your VIVO source directory, run
ant
@ -671,13 +648,12 @@
Go to the "Site Admin" page and click on "Rebuild Search Index" under the
heading "Refresh Content".
</p>
<h3 id="ontology">IV. Ontology Changes</h3>
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
<p>
After Apache Tomcat is started, these files should be reviewed to
verify that the automated upgrade process was executed
successfully.&nbsp; The ontology alignment process will create the
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
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 1.4 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>
@ -685,10 +661,9 @@
</dt>
<dd>
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.
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>
@ -697,43 +672,25 @@
</dt>
<dd>
A log of errors that were encountered during the upgrade
process. This file should be empty if the upgrade was successful.
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>
<dl>
<dt>
<code>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>ontologies/update/changedData/addedData.n3</code>
</dt>
<dd>
An N3 file containing all the statements that were added to
the
knowledge base.
</dd>
</dl>
<h4 id="ontology_knowledge_base">ii. Ontology knowledge base manual
review</h4>
<p>
Changes to the VIVO core ontology may require corresponding
modifications of the knowledge base instance data and local ontology
extensions.
</p>
</p>
<h3 id="kbm">IV. Knowledge Base Migration</h3>
<h4 id="kbmprocess">i.Knowledge Base Migration Process</h4>
<p>
For an description of changes to the VIVO ontology in version 1.4 see the <a href="https://sourceforge.net/apps/mediawiki/vivo/index.php?title=Ontology_changes_from_version_1.3_to_1.4">sourceforge wiki page on ontology changes</a>
</p>
<p>
When Apache Tomcat starts up following the upgrade, it will
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. 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:
changes. The knowledge base migration process will make the following types of changes:
</p>
<dl>
<dt>
@ -741,8 +698,7 @@
</dt>
<dd>
All references to the class (in the subject or object
position)
will be updated to the new name. References to the property will be
position) will be updated to the new name. References to the property will be
updated to the new name.
</dd>
</dl>
@ -760,16 +716,6 @@
directory.
</dd>
</dl>
<dl>
<dt>
Property addition
</dt>
<dd>
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.
</dd>
</dl>
<dl>
<dt>
Annotation property default values
@ -785,6 +731,38 @@
new default value will be propagated to the knowledge base.
</dd>
</dl>
<dl>
<dt>
Structural changes
</dt>
<dd>
Changes in the way individuals (intances of classes) are related to other individuals.
</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>
<h4 id="reviewkbm">ii. Knowledge Base Manual Review for Local Extensions</h4>
Not all of the modifications that may be required are
automated. If you have local extensions to areas of the ontology that have changed, a manual review of the knowledge base is recommended after
the automated upgrade process.
<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"
@ -795,9 +773,10 @@
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>Next Step ...</h3>
<h3 id="nextsteps">Next Steps</h3>
<p>
Now that you have VIVO up and running, please go read the <a href="http://sourceforge.net/apps/mediawiki/vivo/index.php?title=Site_Administrator_Guide">Site Administrator's Guide</a>.
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>
</div>

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productMods/config/listViewConfig-relatedRole.xml
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@ -33,8 +33,9 @@ http://vivoweb.org/ontology/core#realizedRole and http://vivoweb.org/ontology/co
OPTIONAL { ?subclass rdfs:label ?roleTypeLabel }
?roleProp rdfs:subPropertyOf core:roleOf ;
rdfs:domain ?subclass .
?role ?roleProp ?indivInRole
OPTIONAL { ?indivInRole rdfs:label ?indivLabel }
OPTIONAL { ?role ?roleProp ?indivInRole
OPTIONAL { ?indivInRole rdfs:label ?indivLabel }
}
}
OPTIONAL { ?role core:dateTimeInterval ?dateTimeInterval
@ -86,7 +87,7 @@ http://vivoweb.org/ontology/core#realizedRole and http://vivoweb.org/ontology/co
?role vitro:mostSpecificType ?subclass
} UNION {
?subject ?property ?role .
?role a ?subclass .
?role vitro:mostSpecificType ?subclass .
?subclass rdfs:label ?roleTypeLabel
} UNION {
?subject ?property ?role .

1
src/org/vivoweb/webapp/util/ModelUtils.java
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@ -56,6 +56,7 @@ public class ModelUtils {
VClassDao vcd = wadf.getVClassDao();
List<String> superClassURIs = vcd.getSuperClassURIs(classURI, false);
superClassURIs.add(classURI);
Iterator<String> iter = superClassURIs.iterator();
ObjectProperty op = new ObjectProperty();