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Some of the warnings or errors may be cryptic, but they are intended to offer clues as to why your VIVO installation will not work properly.

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FIGURE 1 - A fatal error at startup

Rebuilding the Search Index

The search index of VIVO is used not just for full text search but also for the menu pages and index pages. If the system is not displaying the individuals that you would expect to see, the search index may need to be rebuilt. To rebuild the index log in as an administrative user and request *

http://vivo.example.edu/SearchIndex

*. This page will allow you to start a rebuild of the search index. A rebuild may take some time. The browser page will refresh every few seconds. Once the index rebuild is set up, the page will display how much time the rebuild has taken, and an estimate of how much additional time will be needed. When the indexing is completed, the page will return to its previous state.

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Examples of VIVO web addresses and default namespace values:

To check what your default namespace is currently set for:

1. Log into VIVO as an administrator, go to Site Admin -> SPARQL query.

2. Clear all of the text from the text area, enter the following query in the text area:

   Panelcode
   SELECT str( ?a ) ?b WHERE { ?_ <http ?a <http://vitro.mannlib.cornell.edu/ns/vitro/0. 7#rootTab> ?a 7#rootTab> ?b }

3. Scroll down and click “Run Query” and you should get a result like this:Image Removed
   Image Added

4. To get the default namespace from the result, take everything in quotes braces up to and including the last forward slash. In this case the default namespace is *

   No Formatcode
   http://usertestingvivo.mannlibmydomain.cornell.edu/individual/

   *

5. If you do not have a default namespace that matches If the default namespace does not match the domain name where your VIVO application is installed, you can use follow the steps below:
   1. Use the “Change Namespace of Resources” option under Site Admin – Ingest Tools to
   correct it. If you just change your configuration in runtime.properties, VIVO will not run correctly. Once you’ve made the change in the SiteAdmin, you will need to change it in runtime.properties, re-deploy and restart tomcat.
   1. set the default namespace to match your VIVO application domain name as in the above examples.
   2. Set Vitro.defaultNamespace in runtime.properties to the value for your namespace
   3. Restart Tomcat

Long URLS

If you checked your default namespace and ensured it matches the domain name where your VIVO application is installed, you may find that you still have long URLs on some people profiles.

In other words, you expect to have URLs like this: *

http://vivo.example.edu/individual/n5143

But instead, you have URLs like this:

http://example.edu/individual?uri=http%3A%2F%2Fvivo.example.edu%2Fsomethingl%2Fn5143

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In general, once you have the default namespace set up correctly for your VIVO application, then all the individuals you create using the web interface will have the default namespace. You have to be careful to make sure that any individuals created by an ingest process use the default namespace. Please see the Data Ingest Guide located at http://vivoweb.org for instructions.

Some individuals that are shipped with the application are not in the default namespace. For example, the countries and geographical locations are in a different namespace. Do not attempt to change the namespace of these individuals.