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NIHVIVO-2936 upgrade doc

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stellamit 2011-07-18 18:27:06 +00:00
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doc/upgrade-1.3.html
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@ -40,9 +40,9 @@ page before final release.<br>
<toc> <toc>
<ol class="roman1"> <ol class="roman1">
<li> <a href="#preparation">Before Performing the Upgrade</a> </li> <li> <a href="#preparation">Before Performing the Upgrade</a> </li>
<li> <a href="#triple_store">Triple Store</a> (BL)</li> <li> <a href="#triple_store">Triple Store</a></li>
<li> <a href="#upgrade_process">The Upgrade Process</a> </li> <li> <a href="#upgrade_process">The Upgrade Process</a> </li>
<li> <a href="#ontology">Ontology Changes</a> (SM) <li> <a href="#ontology">Ontology Changes</a>
<ol class="roman2"> <ol class="roman2">
<li> <a href="#verify_ontology_upgrade">Verify Ontology upgrade <li> <a href="#verify_ontology_upgrade">Verify Ontology upgrade
process</a> </li> process</a> </li>
@ -93,9 +93,9 @@ data with the revised ontology. See the section on the <a
<p> VIVO 1.3 now requires you to use Jena's SPARQL database (SDB) for <p> VIVO 1.3 now requires you to use Jena's SPARQL database (SDB) for
the triple store technology.&nbsp; Jena's legacy relational database the triple store technology.&nbsp; Jena's legacy relational database
store (RDB) was used by VIVO 1.1.1 and earlier.&nbsp; Both SDB and RDB store (RDB) was used by VIVO 1.1.1 and earlier.&nbsp; Both SDB and RDB
were available in VIVO 1.2 and 1.2.1.&nbsp; A VIVO 1.2 system running were available in VIVO 1.2 and 1.2.1.&nbsp; A VIVO 1.2[.1] system running
in RDB mode ... [<span style="color: rgb(255, 102, 102);">WHAT HAPPENS in RDB mode will be automatically converted to SDB mode when it is upgraded
IF THEY UPGRADE in RDB MODE? - elly</span>]</p> to VIVO 1.3.</span></p>
<p> SDB mode caches only a fraction of the RDF data in memory. Most <p> SDB mode caches only a fraction of the RDF data in memory. Most
queries are issued directly against the underlying database. This queries are issued directly against the underlying database. This
allows VIVO installations to display data from large RDF models while allows VIVO installations to display data from large RDF models while
@ -105,9 +105,9 @@ to load in SDB mode, and performance will depend on the configuration
parameters of the database server. Additionally, advanced OWL reasoning parameters of the database server. Additionally, advanced OWL reasoning
(not enabled by default in either mode) is not possible in SDB mode. (not enabled by default in either mode) is not possible in SDB mode.
With SDB, only the default set of inferences (inferred rdf:type With SDB, only the default set of inferences (inferred rdf:type
statements) are generated, though they are generated as soon as data is statements) are generated, and they are generated as soon as data is
edited rather than in a background process. </p> edited rather than in a background process. </p>
<p> This copying process can take a number of hours to complete if the <p> A conversion from RDB to SDB mode can take a number of hours to complete if the
installation contains a large amount of RDF data (roughly a million installation contains a large amount of RDF data (roughly a million
triples or more). See section <a href="#setup_sdb">Set Up SDB Store in triples or more). See section <a href="#setup_sdb">Set Up SDB Store in
the Background (Optional)</a> for instructions on how to run this the Background (Optional)</a> for instructions on how to run this
@ -422,7 +422,7 @@ successfully.&nbsp; The ontology alignment process will create the
following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>: following files in the Tomcat <code>webapps/vivo/WEB-INF directory</code>:
</p> </p>
<dl> <dl>
<dt> <code>ontologies/update/logs/knowledgeBaseUpdate.log</code> </dt> <dt> <code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).log</code> </dt>
<dd> A log of a summary of updates that were made to the knowledge <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 base and notes about some recommended manual reviews. This file should
end with "Finished knowledge base migration". If this file contains any end with "Finished knowledge base migration". If this file contains any
@ -430,7 +430,7 @@ warnings they should be reviewed with your implementation team
representative to see whether any corrective action needs to be taken. </dd> representative to see whether any corrective action needs to be taken. </dd>
</dl> </dl>
<dl> <dl>
<dt> <code>ontologies/update/logs/knowledgeBaseUpdate.error.log</code> <dt> <code>ontologies/update/logs/knowledgeBaseUpdate.(timestamp).error.log</code>
</dt> </dt>
<dd> A log of errors that were encountered during the upgrade <dd> A log of errors that were encountered during the upgrade
process. This file should be empty if the upgrade was successful. </dd> process. This file should be empty if the upgrade was successful. </dd>
@ -464,7 +464,7 @@ updated to the new name. </dd>
</dl> </dl>
<dl> <dl>
<dt> Class or Property deletion </dt> <dt> Class or Property deletion </dt>
<dd> All individuals in a deleted class will be removed. <br> <dd> All type assertions of a deleted class will be removed. <br>
All statements using a deleted property will be changed to use the All statements using a deleted property will be changed to use the
nearest available superproperty. If there is no available superproperty nearest available superproperty. If there is no available superproperty
then the statement will be deleted from the knowledge base. Note that then the statement will be deleted from the knowledge base. Note that