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Adding the text from Brian about SDB to install.html (one section) and upgrade-1.2.html (2 sections).

Browse source 
Also added a new intro sentence to Pellet reasoner section.
Completes Jira NIHVIVO-1782
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ejc12 2011-02-10 04:23:54 +00:00
parent 6e65e2bb83
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211
doc/install.html
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@ -2,9 +2,9 @@
<html lang="en"> <html lang="en">
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<title>VIVO</title> <title>VIVO Release 1 V1.2 Installation Guide</title>
<link rel="stylesheet" href="./css/doc.css" media="screen" /> <link rel="stylesheet" href="./css/doc.css" media="screen" />
<link rel="stylesheet" href="./css/print.css" media="print" /> <link rel="stylesheet" href="./css/print.css" media="print" />
</head> </head>
<body> <body>
<div id="branding" role="banner"> <div id="branding" role="banner">
@ -34,9 +34,8 @@
release also features two new visualization options: temporal graphing release also features two new visualization options: temporal graphing
for organizations, and personal visualizations extended to cover grants for organizations, and personal visualizations extended to cover grants
as well as publications. The VIVO Harvester library has also been as well as publications. The VIVO Harvester library has also been
significantly improved and expanded in scope for its 1.0 release significantly improved and expanded in scope for its 1.0 release
through the VIVO SourceForge project at through the VIVO SourceForge project at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p> </p>
<h4>Templating system for page generation, navigation, and theming</h4> <h4>Templating system for page generation, navigation, and theming</h4>
<p> <p>
@ -54,8 +53,8 @@
</p> </p>
<h4>Storage model</h4> <h4>Storage model</h4>
<p> <p>
While server memory capacity has increased significantly in recent While server memory capacity has increased significantly in recent
years, VIVO's reliance on in-memory caching of RDF data had put limits years, VIVO's reliance on in-memory caching of RDF data had put limits
on the ultimate scalability of VIVO instances and potentially increased on the ultimate scalability of VIVO instances and potentially increased
the cost of servers required to support VIVO.&nbsp; the cost of servers required to support VIVO.&nbsp;
<br> <br>
@ -77,10 +76,10 @@
</p> </p>
<h4>Ontology</h4> <h4>Ontology</h4>
<p> <p>
VIVO 1.2 includes a new ontology module representing research VIVO 1.2 includes a new ontology module representing research
resources including biological specimens, human studies, instruments, resources including biological specimens, human studies, instruments,
organisms, protocols, reagents, and research opportunities. This module organisms, protocols, reagents, and research opportunities. This module
is aligned with the top-level ontology classes and properties from the is aligned with the top-level ontology classes and properties from the
NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>. NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
</p> </p>
<h3>Associated VIVO releases</h3> <h3>Associated VIVO releases</h3>
@ -88,9 +87,8 @@
<p> <p>
The Harvester development team is releasing version 1.0 of the VIVO The Harvester development team is releasing version 1.0 of the VIVO
Harvester library, an extensible data ingest and updating framework Harvester library, an extensible data ingest and updating framework
with sample configurations for loading PubMed publication, grants, and with sample configurations for loading PubMed publication, grants, and
human resources data. The Harvester is available at human resources data. The Harvester is available at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p> </p>
<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2> <hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
<p> <p>
@ -101,9 +99,9 @@
<ul> <ul>
<li> <li>
These instructions assume that you are performing a clean These instructions assume that you are performing a clean
install, including emptying an existing database and removing a install, including emptying an existing database and removing a
previous installation from the Tomcat webapps directory. Product previous installation from the Tomcat webapps directory. Product
functionality may not be as expected if you install over an existing functionality may not be as expected if you install over an existing
installation of an earlier version. installation of an earlier version.
</li> </li>
<li> <li>
@ -129,7 +127,7 @@
<a href="#download_code">Download the VIVO Application Source</a> <a href="#download_code">Download the VIVO Application Source</a>
</li> </li>
<li> <li>
<a href="#data_storage">SDB vs RDB</a> <a href="#triple_store">Choose Triple Store</a>
</li> </li>
<li> <li>
<a href="#deploy_properties">Specify deployment properties</a> <a href="#deploy_properties">Specify deployment properties</a>
@ -211,11 +209,11 @@
of of
the time, the hostname will equal <code>localhost</code>. the time, the hostname will equal <code>localhost</code>.
</p> </p>
<pre> CREATE DATABASE dbname CHARACTER SET utf8;<br> </pre> <pre> CREATE DATABASE dbname CHARACTER SET utf8;<br></pre>
<p> <p>
Grant access to a database user. For example: Grant access to a database user. For example:
</p> </p>
<pre> GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';<br> </pre> <pre> GRANT ALL ON dbname.* TO 'username'@'hostname' IDENTIFIED BY 'password';<br></pre>
<p> <p>
Keep track of the database name, username, and password for Step Keep track of the database name, username, and password for Step
IV. IV.
@ -230,9 +228,30 @@
<br> <br>
<a href="http://vivoweb.org/download">http://vivoweb.org/download</a> <a href="http://vivoweb.org/download">http://vivoweb.org/download</a>
</p> </p>
<h3 id="data_storage">IV. SDB vs RDB (title)</h3> <h3 id="triple_store">IV. Choose Triple Store</h3>
<p> <p>
Content from Brian Lowe coming. VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by
Jena's legacy relational database store (RDB) and Jena's SPARQL database (SDB). RDB was
used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the
entire RDF model in the server's main memory. The memory available to VIVO limits the
number of RDF statements that may be stored.
</p>
<p>
SDB mode caches only a fraction of the RDF data in memory. Most queries are issued directly
against the underlying database. This allows VIVO installations to display data from large
RDF models while requiring only a small amount of server memory to run the application.
There is a tradeoff in response time: pages make take slightly longer to load in SDB mode,
and performance will depend on the configuration parameters of the database server.
Additionally, advanced OWL reasoning (not enabled by default in either mode) is not possible
in SDB mode. With SDB, only the default set of inferences (inferred rdf:type statements) are
generated, though they are generated as soon as data is edited rather than in a background process.
</p>
<p>
Though a VIVO installation may be switched back and forth between RDB and SDB mode by changing
a configuration property and redeploying the application, it is important to note that data
added in one mode will not typically appear in the other. The exception is when a system is
first switched from RDB mode to SDB mode. In this case, the data from the RDB store will be
automatically migrated to SDB.
</p> </p>
<h3 id="deploy_properties">V. Specify deployment properties </h3> <h3 id="deploy_properties">V. Specify deployment properties </h3>
<p> <p>
@ -276,8 +295,8 @@
"http://vivo.example.edu/individual/" in order to support linked data. "http://vivo.example.edu/individual/" in order to support linked data.
Similarly, if VIVO is installed at "http://www.example.edu/vivo" the Similarly, if VIVO is installed at "http://www.example.edu/vivo" the
default namespace must be set to default namespace must be set to
"http://www.example.edu/vivo/individual/"<h5>* The namespace must end with "individual/" (including the "http://www.example.edu/vivo/individual/"<h5>* The namespace must end with
trailing slash).</h5> "individual/" (including the trailing slash).</h5>
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">
@ -466,9 +485,9 @@
<tr> <tr>
<td colspan="2"> <td colspan="2">
Change the dbtype setting to use a database Change the dbtype setting to use a database
other than MySQL. Otherwise, leave this value unchanged. Possible other than MySQL. Otherwise, leave this value unchanged. Possible
values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and values are DB2, derby, HSQLDB, H2, MySQL, Oracle, PostgreSQL, and
SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported SQLServer. Refer to http://openjena.org/wiki/SDB/Databases_Supported
for additional information. for additional information.
</td> </td>
</tr> </tr>
@ -597,8 +616,8 @@
</p> </p>
<pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre> <pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre>
<p> <p>
This sets Tomcat to allocate an initial heap of 2048 megabytes, a This sets Tomcat to allocate an initial heap of 2048 megabytes, a
maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024 maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024
megabytes is a minimum practical heap size for production installations megabytes is a minimum practical heap size for production installations
storing data for large academic institutions, and additional heap space storing data for large academic institutions, and additional heap space
is preferable. For testing with small sets of data, 256m to 512m should is preferable. For testing with small sets of data, 256m to 512m should
@ -635,17 +654,17 @@
will be prompted to select a new password and verify it a second time. will be prompted to select a new password and verify it a second time.
</p> </p>
<p> <p>
After verifying your new password, you will be presented with a After verifying your new password, you will be presented with a
menu of editing options. Here you can create OWL classes, object menu of editing options. Here you can create OWL classes, object
properties, data properties, and configure the display of data. properties, data properties, and configure the display of data.
Currently, any classes you wish to make visible on your website must be Currently, any classes you wish to make visible on your website must be
part of a class group, and there a number of visibility and display part of a class group, and there a number of visibility and display
options available for each ontology entity. VIVO comes with a core VIVO options available for each ontology entity. VIVO comes with a core VIVO
ontology, but you may also upload other ontologies from an RDF file. ontology, but you may also upload other ontologies from an RDF file.
</p> </p>
<p> <p>
Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note
that Vitro currently works best with OWL-DL ontologies and has only that Vitro currently works best with OWL-DL ontologies and has only
limited support for pure RDF data. You can enter a URL pointing to the limited support for pure RDF data. You can enter a URL pointing to the
RDF data you wish to load or upload a file on your local machine. RDF data you wish to load or upload a file on your local machine.
Ensure that the "add RDF" radio button is selected. You will also Ensure that the "add RDF" radio button is selected. You will also
@ -670,9 +689,9 @@
</p> </p>
<p> <p>
Log in as a system administrator. Navigate to the "Site Admin" Log in as a system administrator. Navigate to the "Site Admin"
table of contents (link in the right side of the header). Go to "Site table of contents (link in the right side of the header). Go to "Site
Information" (under "Site Configuration"). In the "Site Information Information" (under "Site Configuration"). In the "Site Information
Editing Form," enter a functional email address in the field "Contact Editing Form," enter a functional email address in the field "Contact
Email Address." and submit the change. Email Address." and submit the change.
</p> </p>
<p> <p>
@ -703,9 +722,9 @@
<p> <p>
After setting up the mod_jk connector above, you will need to After setting up the mod_jk connector above, you will need to
modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>) modify the Tomcat's server.xml (located in <code>[tomcat root]/conf/</code>)
to to
respond respond
to requests from Apache via the connector. Look for the to requests from Apache via the connector. Look for the
&lt;connector&gt; directive and add the following properties: &lt;connector&gt; directive and add the following properties:
</p> </p>
<pre> connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"&nbsp; <br> </pre> <pre> connectionTimeout="20000" maxThreads="320" keepAliveTimeout="20000"&nbsp; <br> </pre>
@ -719,14 +738,30 @@
directive directive
and update as follows: and update as follows:
</p> </p>
<pre> &lt;Host name="localhost" appBase="webapps"<br> DeployOnStartup="false"<br> unpackWARs="true" autoDeploy="false"<br> xmlValidation="false" xmlNamespaceAware="false"&gt;<br> <br> &lt;Alias&gt;example.com&lt;/Alias&gt;<br> &lt;Context path=""<br> docBase="/usr/local/tomcat/webapps/vivo"<br> reloadable="true"<br> cookies="true" &gt;<br> &lt;Manager pathname="" /&gt;<br> &lt;Environment type="java.lang.String" override="false" <br> name="path.configuration" <br> value="deploy.properties"<br> /&gt;<br> &lt;/Context&gt;<br> ...<br> </pre> <pre>
&lt;Host name="localhost" appBase="webapps"<br>
DeployOnStartup="false"<br>
unpackWARs="true" autoDeploy="false"<br>
xmlValidation="false" xmlNamespaceAware="false"&gt;<br> <br>
&lt;Alias&gt;example.com&lt;/Alias&gt;<br>
&lt;Context path=""<br>
docBase="/usr/local/tomcat/webapps/vivo"<br>
reloadable="true"<br>
cookies="true" &gt;<br>
&lt;Manager pathname="" /&gt;<br>
&lt;Environment type="java.lang.String" override="false" <br>
name="path.configuration" <br>
value="deploy.properties"<br>
/&gt;<br>
&lt;/Context&gt;<br>
...
</pre>
<h3 id="pellet">XII. Configure Pellet Reasoner </h3> <h3 id="pellet">XII. Configure Pellet Reasoner </h3>
<p> <p>
<em>Do we need this section still? - elly</em> This optional configuration step is only applicable to VIVO installations
</p> running in RDB mode (See section <a href="triple_store">Choose Triple Store</a> for details).
<p> VIVO uses the Pellet engine to perform reasoning, which runs in the
VIVO uses the Pellet engine to perform reasoning, which runs in the background at startup and also when the knowledge base is edited. VIVO
background at startup and also when the knowledge base is edited. VIVO
continues serving pages while the reasoner continues working; when the continues serving pages while the reasoner continues working; when the
reasoner finishes, the new inferences appear. Inferred statements are reasoner finishes, the new inferences appear. Inferred statements are
cached in a database graph so that they are available immediately when cached in a database graph so that they are available immediately when
@ -734,9 +769,9 @@
</p> </p>
<p> <p>
By default, Pellet is fed only an incomplete view of your ontology By default, Pellet is fed only an incomplete view of your ontology
and only certain inferences are materialized. These include rdf:type, and only certain inferences are materialized. These include rdf:type,
rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode rdfs:subClassOf, owl:equivalentClass, and owl:disjointWith. This mode
is typically suitable for ontologies with a lot of instance data. If is typically suitable for ontologies with a lot of instance data. If
you would like to keep the default mode, skip to the next step. you would like to keep the default mode, skip to the next step.
</p> </p>
<p> <p>
@ -835,9 +870,9 @@
privileges assigned to that account. privileges assigned to that account.
<p> <p>
In addition, VIVO will try to associate the user with a profile In addition, VIVO will try to associate the user with a profile
page, so the user may edit his own profile data. VIVO will search the page, so the user may edit his own profile data. VIVO will search the
data model for a person with a property that matches the User’s network data model for a person with a property that matches the User’s network
ID. You need to tell VIVO what property should be used for matching. ID. You need to tell VIVO what property should be used for matching.
Insert a line like this in the deploy.properties file: Insert a line like this in the deploy.properties file:
</p> </p>
<pre>selfEditing.idMatchingProperty = [the URI of the property]</pre> <pre>selfEditing.idMatchingProperty = [the URI of the property]</pre>
@ -865,10 +900,10 @@
</p> </p>
<ul> <ul>
<li> <li>
Click on the "Index" link on the upper right, below the logo. Click on the "Index" link on the upper right, below the logo.
You should see a "locations" section, with links for "Country" and You should see a "locations" section, with links for "Country" and
"Geographic Location." The index is built in a background thread, so on "Geographic Location." The index is built in a background thread, so on
your first login, you may see an empty index instead. Refresh the page your first login, you may see an empty index instead. Refresh the page
periodically to see whether the index will be populated. This may take periodically to see whether the index will be populated. This may take
some time: with VIVO installed on a modest laptop computer, loading the some time: with VIVO installed on a modest laptop computer, loading the
ontology files and building the index took more than 5 minutes from the ontology files and building the index took more than 5 minutes from the
@ -903,14 +938,14 @@
</li> </li>
<li> <li>
Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>. Open a new web browser or browser tab to the page <a href="http://marbles.sourceforge.net/">http://marbles.sourceforge.net/</a>.
In In
the the
pink box on that page enter the URI of the individual you pink box on that page enter the URI of the individual you
created in the previous step and click "open." created in the previous step and click "open."
</li> </li>
<li> <li>
In the resulting page search for the URI of the "test In the resulting page search for the URI of the "test
individual." You should find it towards the bottom of the page next to individual." You should find it towards the bottom of the page next to
a red dot followed by "redirect (303)." This indicates that you are a red dot followed by "redirect (303)." This indicates that you are
successfully serving linked RDF data. If the URI of the "test successfully serving linked RDF data. If the URI of the "test
individual" is followed by "failed (400)" you are not successfully individual" is followed by "failed (400)" you are not successfully
@ -923,36 +958,36 @@
<ul> <ul>
<li> <li>
Type the word "Australia" into the search box, and click on the Type the word "Australia" into the search box, and click on the
Search button.You should see a page of results, with links to countries Search button.You should see a page of results, with links to countries
that border Australia, individuals that include Australia, and to that border Australia, individuals that include Australia, and to
Australia itself. To trigger the search index, you can log in as a site Australia itself. To trigger the search index, you can log in as a site
administrator and go to "http://your-vivo-url/SearchIndex". administrator and go to "http://your-vivo-url/SearchIndex".
</li> </li>
</ul> </ul>
</div> </div>
<!-- #wrapper-content --> <!-- #wrapper-content -->
<div id="footer" role="contentinfo"> <div id="footer" role="contentinfo">
<p class="copyright"> <p class="copyright">
<small> <small>
&copy;2011 &copy;2011
All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a> All Rights Reserved | <a class="terms" href="/termsOfUse">Terms of Use</a>
</small> </small>
| Powered | Powered
by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a> by <a class="powered-by-vivo" href="http://vivoweb.org" target="_blank"><strong>VIVO</strong></a>
</p> </p>
<div id="nav" role="navigation"> <div id="nav" role="navigation">
<ul id="footer-nav" role="list"> <ul id="footer-nav" role="list">
<li role="listitem"> <li role="listitem">
<a href="http://vivoweb.org/about">About</a> <a href="http://vivoweb.org/about">About</a>
</li> </li>
<li role="listitem"> <li role="listitem">
<a href="http://vivoweb.org/contact">Contact Us</a> <a href="http://vivoweb.org/contact">Contact Us</a>
</li> </li>
<li role="listitem"> <li role="listitem">
<a href="http://www.vivoweb.org/support" target="blank">Support</a> <a href="http://www.vivoweb.org/support" target="blank">Support</a>
</li> </li>
</ul> </ul>
</nav> </nav>
</div> </div>
</body> </body>
</html> </html>

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@ -2,7 +2,7 @@
<html lang="en"> <html lang="en">
<head> <head>
<meta charset="utf-8" /> <meta charset="utf-8" />
<title>VIVO</title> <title>VIVO Release 1 V1.2 Upgrade Guide</title>
<link rel="stylesheet" href="./css/doc.css" media="screen" /> <link rel="stylesheet" href="./css/doc.css" media="screen" />
<link rel="stylesheet" href="./css/print.css" media="print" /> <link rel="stylesheet" href="./css/print.css" media="print" />
</head> </head>
@ -90,8 +90,8 @@
</p> </p>
<h4>Ontology</h4> <h4>Ontology</h4>
<p> <p>
VIVO 1.2 includes a new ontology module representing research VIVO 1.2 includes a new ontology module representing research
resources including biological specimens, human studies, instruments, resources including biological specimens, human studies, instruments,
organisms, protocols, reagents, and research opportunities. This module organisms, protocols, reagents, and research opportunities. This module
is aligned with the top-level ontology classes and properties from the is aligned with the top-level ontology classes and properties from the
NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>. NIH-funded <a href="https://www.eagle-i.org/home/">eagle-i Project</a>.
@ -109,6 +109,9 @@
<ol class="roman1"> <ol class="roman1">
<li> <li>
<a href="#preparation">Before Performing the Upgrade</a> <a href="#preparation">Before Performing the Upgrade</a>
</li>
<li>
<a href="#triple_store">Chose Triple Store</a>
</li> </li>
<li> <li>
<a href="#upgrade_process">The Upgrade Process</a> <a href="#upgrade_process">The Upgrade Process</a>
@ -141,6 +144,9 @@
</li> </li>
<li> <li>
<a href="#theme">Theme Modifications</a> <a href="#theme">Theme Modifications</a>
</li>
<li>
<a href="#setup_sdb">Set Up SDB Store in the Background (Optional)</a>
</li> </li>
</ol> </ol>
</toc> </toc>
@ -188,7 +194,46 @@
below for more information. below for more information.
</li> </li>
</ul> </ul>
<h3 id="upgrade_process">II. The Upgrade Process</h3> <h3 id="triple_store">II. Choose Triple Store</h3>
<p>
VIVO 1.2 offers a choice of two triple store technologies: in-memory models backed by
Jena's legacy relational database store (RDB) and Jena's SPARQL database (SDB). RDB was
used by VIVO 1.1.1 and earlier. This mode offers fast response, but only by caching the
entire RDF model in the server's main memory. The memory available to VIVO limits the
number of RDF statements that may be stored.
</p>
<p>
SDB mode caches only a fraction of the RDF data in memory. Most queries are issued directly
against the underlying database. This allows VIVO installations to display data from large
RDF models while requiring only a small amount of server memory to run the application.
There is a tradeoff in response time: pages make take slightly longer to load in SDB mode,
and performance will depend on the configuration parameters of the database server.
Additionally, advanced OWL reasoning (not enabled by default in either mode) is not possible
in SDB mode. With SDB, only the default set of inferences (inferred rdf:type statements) are
generated, though they are generated as soon as data is edited rather than in a background process.
</p>
<p>
Though a VIVO installation may be switched back and forth between RDB and SDB mode by changing
a configuration property and redeploying the application, it is important to note that data
added in one mode will not typically appear in the other. The exception is when a system is
first switched from RDB mode to SDB mode. In this case, the data from the RDB store will be
automatically migrated to SDB.
</p>
<p>
A VIVO 1.2 system that is upgraded from VIVO 1.1.1 must initially be run in RDB mode in order
receive required ontology updates. Attempting to run an upgraded system initially in SDB will
result in a logged error message, and the application will not start. After the system starts
up successfully the first time in RDB mode, it may then be switched to SDB, redeployed, and restarted.
Upon restart, the data in the RDB store will be copied to the SDB store.
</p>
<p>
This copying process can take a number of hours to complete if the 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 the Background (Optional)</a> for instructions on how
to run this lengthy conversion process in the background while an RDB system is operating.
Doing this will reduce the time necessary to start VIVO the first time it is run in SDB mode.
</p>
<h3 id="upgrade_process">III. The Upgrade Process</h3>
<p> <p>
1. Download the new distribution file and unpack it into a new 1. Download the new distribution file and unpack it into a new
source directory. source directory.
@ -578,7 +623,7 @@
<p> <p>
6. Start Apache Tomcat and log in to VIVO. 6. Start Apache Tomcat and log in to VIVO.
</p> </p>
<h3 id="ontology">III. Ontology Changes</h3> <h3 id="ontology">IV. Ontology Changes</h3>
<h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4> <h4 id="verify_ontology_upgrade">i. Verify Ontology upgrade process</h4>
<p> <p>
After Apache Tomcat is started, these files should be reviewed to After Apache Tomcat is started, these files should be reviewed to
@ -591,8 +636,8 @@
<code>ontologies/update/logs/knowledgeBaseUpdate.log</code> <code>ontologies/update/logs/knowledgeBaseUpdate.log</code>
</dt> </dt>
<dd> <dd>
A log of a summary of updates that were made to the knowledge base and 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 notes about some recommended manual reviews. This file should end with
"Finished knowledge base migration". "Finished knowledge base migration".
If this file contains any warnings they should be reviewed with If this file contains any warnings they should be reviewed with
your implementation team representative to see whether any your implementation team representative to see whether any
@ -688,7 +733,7 @@
new default value will be propagated to the knowledge base. new default value will be propagated to the knowledge base.
</dd> </dd>
</dl> </dl>
<h3 id="fileSystem">IV. File Storage System Upgrade</h3> <h3 id="fileSystem">V. File Storage System Upgrade</h3>
<h4 id="changes_to_storage">i. Changes to the File Storage System</h4> <h4 id="changes_to_storage">i. Changes to the File Storage System</h4>
<p> <p>
Each uploaded file exists as an individual entity in VIVO. When the Each uploaded file exists as an individual entity in VIVO. When the
@ -726,7 +771,7 @@
corrective action needs to be taken. corrective action needs to be taken.
</dd> </dd>
</dl> </dl>
<h3 id="theme">V. Theme Changes</h3> <h3 id="theme">VI. Theme Changes</h3>
<h4 style="color:red">Need Nick to help with this section</h4> <h4 style="color:red">Need Nick to help with this section</h4>
<p> <p>
VIVO 1.2 comes with a new theme called "wilma" that uses the FreeMarker template VIVO 1.2 comes with a new theme called "wilma" that uses the FreeMarker template
@ -831,6 +876,32 @@
your 1.2 theme. your 1.2 theme.
</dd> </dd>
</dl> </dl>
<h3 id="setup_sdb">VII. Set Up SDB Store in the Background (Optional)</h3>
<p>
If your VIVO installation is running in RDB mode, and you'd like to convert
to SDB, you can start the conversion process in the background while the RDB
system is running. This will reduce the delay in initial startup after the
application is redeployed with deploy.properties set for SDB. Note that it
is important not to edit any data anywhere in the application while this
background conversion is running.
</p>
<p>
To start the SDB conversion, log in as a system
administrator and request /sdbsetup. (For example, if your VIVO is installed
at http://vivo.myuniversity.edu/ you would type
http://vivo.myuniversity.edu/sdbsetup into your browser.)
</p>
<p>
Click the button that appears on this page.
</p>
<p>
During the course of the SDB setup, which may take several hours on a
large database, subsequent requests to /sdbsetup will display a
message that the operation is still in progress. When a request for this
page shows a message that the SDB setup has completed successfully, shut down
Tomcat, set deploy.properties to SDB mode, redeploy, and restart Tomcat.
VIVO will now be running from the SDB store.
</p>
</div> </div>
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