NIHVIVO-3103 corrections and reformatting.
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j2blake
parent
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commit
535bb3bbfc
3 changed files with 33 additions and 96 deletions
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@ -28,7 +28,7 @@ body{
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margin: 0 auto;
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}
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body{
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background: #f3f3f0 url(../images/header-background.png) center 0 no-repeat;
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background: #fff url(../images/header-background.gif) center 0 repeat-x;
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}
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/* h1,h2,h3,h4,h5,h6 ------> */
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h1 {
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BIN
doc/images/header-background.gif
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doc/images/header-background.gif
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After Width: | Height: | Size: 194 B |
127
doc/install.html
127
doc/install.html
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@ -334,21 +334,6 @@
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http://vivo.mydomain.edu/individual/
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Directory where Vitro code is located. In most
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deployments, this is set to ./vitro-core (It is not uncommon for this
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setting to point elsewhere in development environments).
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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vitro.core.dir
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</td>
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<td>
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./vitro-core
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</td>
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</tr>
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<tr>
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<td colspan="2">
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Directory where tomcat is installed.
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@ -654,71 +639,12 @@
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remote_userID
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</td>
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</tr>
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<tr>
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<td colspan="2">
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The temporal graph visualization can require
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extensive machine resources. This can have a particularly noticable
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impact on memory usage if
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<ul>
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<li>
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The organization tree is deep,
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</li>
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<li>
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The number of grants and publications is large.
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</li>
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</ul>
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VIVO V1.3 mitigates this problem by the way of a caching
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mechanism and hence we can safely set this to be enabled by default.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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visualization.temporal
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</td>
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<td>
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enabled
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</td>
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</tr>
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<tr>
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<td colspan="2">
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The temporal graph visualization is used to
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compare different organizations/people within an organization on
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parameters like number of publications or grants. By default, the app
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will attempt to make its best guess at the top level organization in
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your instance. If you're unhappy with this selection, uncomment out the
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property below and set it to the URI of the organization individual you
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want to identify as the top level organization. It will be used as the
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default whenever the temporal graph visualization is rendered without
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being passed an explicit org. For example, to use "Ponce School of
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Medicine" as the top organization:
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<br>
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<code>visualization.topLevelOrg =
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http://vivo.psm.edu/individual/n2862</code>
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<br>
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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visualization.topLevelOrg
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</td>
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<td>
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http://vivo-trunk.indiana.edu/individual/topLevelOrgURI
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</td>
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</tr>
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<tr>
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<td colspan="2">
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An absolute file path, pointing to the root directory of the Harvester utility.
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You must include the final slash.
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</td>
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</tr>
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<tr class="odd_row">
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<td>
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harvester.location
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</td>
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<td>
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/usr/local/vivo/harvester/
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</td>
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</tr>
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</tbody>
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</table>
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<h3 id="deploy">V. Compile and deploy</h3>
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@ -733,12 +659,12 @@
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<h3 id="tomcat_settings">VI. Set Tomcat JVM parameters and security
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limits</h3>
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<p>
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Currently, VIVO copies the contents of your RDF database into
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VIVO copies small sections of your RDF database into
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memory in order to serve Web requests quickly (the in-memory copy and
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the underlying database are kept in synch as edits are performed).
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</p>
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<p>
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VIVO will require more memory than that allocated to Tomcat by
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VIVO may require more memory than that allocated to Tomcat by
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default. With most installations of Tomcat, the "setenv.sh" or
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"setenv.bat" file in Tomcat's bin directory is a convenient place to
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set the memory parameters. <em>If this file does not exist in Tomcat's
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@ -746,14 +672,11 @@
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<br>
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For example:
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</p>
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<pre> export CATALINA_OPTS="-Xms2048m -Xmx1024m -XX:MaxPermSize=128m"<br> </pre>
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<pre> export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m"<br> </pre>
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<p>
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This sets Tomcat to allocate an initial heap of 2048 megabytes, a
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maximum heap of 1024 megabytes, and a PermGen space of 128 megs. 1024
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megabytes is a minimum practical heap size for production installations
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storing data for large academic institutions, and additional heap space
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is preferable. For testing with small sets of data, 256m to 512m should
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be sufficient.
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This sets Tomcat to allocate an initial heap of 512 megabytes, a
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maximum heap of 512 megabytes, and a PermGen space of 128 megs. Lower
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values may suffice, especially for small test installations.
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</p>
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<p>
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If an OutOfMemoryError is encountered during VIVO execution, it can
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@ -795,8 +718,8 @@
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properties, data properties, and configure the display of data.
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Currently, any classes you wish to make visible on your website must be
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part of a class group, and there are a number of visibility and display
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options available for each ontology entity. VIVO comes with a core VIVO
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ontology, but you may also upload other ontologies from an RDF file.
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options available for each ontology entity. Vitro comes with a minimal
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ontology. You will likely want to upload additional ontologies from an RDF file.
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</p>
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<p>
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Under the "Advanced Data Tools" click "Add/Remove RDF Data." Note
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@ -810,10 +733,7 @@
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Clicking the "Index" tab in the navigation bar at the top right of
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the page will show a simple index of the knowledge base.
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</p>
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<p>
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See more documentation for configuring VIVO, ingesting data, and
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manually adding data at <a href="http://vivoweb.org/support">http://vivoweb.org/support</a>.
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</p>
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<h3 id="contact_email">IX. Set the Contact Email Address (if using
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"Contact Us" form)</h3>
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<p>
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@ -875,7 +795,28 @@
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directive
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and update as follows:
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</p>
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<pre> <br> <Host name="localhost" appBase="webapps"<br> <br> DeployOnStartup="false"<br> <br> unpackWARs="true" autoDeploy="false"<br> <br> xmlValidation="false" xmlNamespaceAware="false"><br> <br> <br> <Alias>example.com</Alias><br> <br> <Context path=""<br> <br> docBase="/usr/local/tomcat/webapps/vivo"<br> <br> reloadable="true"<br> <br> cookies="true" ><br> <br> <Manager pathname="" /><br> <br> <Environment type="java.lang.String" override="false" <br> <br> name="path.configuration" <br> <br> value="deploy.properties"<br> <br> /><br> <br> </Context><br> <br> ...<br> </pre>
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<pre> <Host name="localhost" appBase="webapps"
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DeployOnStartup="false"
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unpackWARs="true" autoDeploy="false"
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xmlValidation="false" xmlNamespaceAware="false">
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<Alias>example.com</Alias>
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<Context path=""
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docBase="/usr/local/tomcat/webapps/vivo"
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reloadable="true"
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cookies="true" >
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<Manager pathname="" />
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<Environment type="java.lang.String" override="false"
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name="path.configuration"
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value="deploy.properties"
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/>
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</Context>
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...
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</pre>
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<h3 id="external_auth">XI. Using an External Authentication System
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with VIVO </h3>
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<p>
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@ -954,11 +895,7 @@
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<li>
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<h5>Associating a User with a profile page.</h5>
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<p>
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If VIVO has an account for the user, the user will be given the
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privileges assigned to that account.
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</p>
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<p>
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In addition, VIVO will try to associate the user with a profile
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VIVO will try to associate the user with a profile
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page, so the user may edit his own profile data. VIVO will search the
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data model for a person with a property that matches the User’s network
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ID (the value of the property must be either a String literal or an
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