[MOBY-guts] biomoby commit

[Eddie Kawas]

kawas
Tue Sep 11 12:48:27 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv6310/Java/docs

Modified Files:
	ConfigureRDFAgent.html 
Log Message:

moby-live/Java/docs ConfigureRDFAgent.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2006/10/05 15:32:47	1.3
+++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2007/09/11 16:48:27	1.4
@@ -29,14 +29,15 @@
   using 'mail', a UNIX/Linux/*nix email client. Moreover, The agent can choose to 
   ignore those services that do not contain signature urls or to remove 
   them.</p>
-</p>
+<p></p>
 <h4>This document is broken down into the following sections: </h4>
 <ul>
   <li><a href="#getting_started">Getting Started</a></li>
   <li><a href="#configuring_the_agent">Configuring the Agent</a></li>
   <li><a href="#setting_up_a_cron_job">Setting up a Cron Job</a></li>
-  <li><a href="moby_admin_dispatcher">MOBY-Admin Dispatcher</a></li>
+  <li><a href="#moby_admin_dispatcher">MOBY-Admin Dispatcher</a></li>
   <li><a href="#uses_for_the_agent">Uses for the Agent</a></li>
+  <li><a href="#faq">FAQ</a></li>
 </ul>
 <p>&nbsp;</p>
 <h3><a name="getting_started"></a>Getting Started</h3>
@@ -86,7 +87,7 @@
       <br>
     These variable must be set for the agent to work properly with these scripts.<br>
     <br>
-    <span class="note">Also, note that it is important to place the variable <strong>JAVA_HOME</strong> in the environment of the web server you are using so that Mobycentral can access it!</span> <br>
+    <span class="note">Also, note that it is <strong>important</strong> to place the variable <strong>JAVA_HOME</strong> in the environment of the web server you are using so that Mobycentral can access it!</span> <br>
       <br>
     </li>
     <li class="dcount"> Add the path to the RDFagent to the <b class="step">[mobycentral]</b> section of your mobycentral.config file:
@@ -411,7 +412,7 @@
 </blockquote>
 <p>This file must be called '.htaccess'.<br>
   <br>
-  Assuming that the MOBY-Admin.pl file is located in the cgi-bin directory of apache, you will have to add the following line to http.conf where the cgi-bin directory is defined:</p>
+  Assuming that the MOBY-Admin.pl file is located in the cgi-bin directory of apache, you will have to add the following line to httpd.conf where the cgi-bin directory is defined:</p>
 <p> <b class="step">AllowOverride AuthConfig</b></p>
 <p> <em>i.e. </em><br>
 </p>
@@ -440,11 +441,11 @@
     file at <em><strong>/path/that/exists/</strong></em></p>
   <p><em><strong>username</strong></em> would be the newly created login name</p>
 </blockquote>
-<p>You will be prompted for a password.<br>
+<p>You will be prompted for a password.<br/>
 <p class="note"> This login name and password will have to be entered into the agents 
   configuration file. </p>
 </p>
-</p>
+<strong>Don't forget to restart apache each and every time that you modify the httpd.conf file!</strong>
 <h3><a name="uses_for_the_agent"></a>Uses for the Agent</h3>
 <p>The following are some uses for the agent:</p>
 <ol>
@@ -472,6 +473,20 @@
 </ol>
 <p><br>
   If you have any other uses for the agent, please let me know.</p>
+  
+<h3><a name="faq"></a>FAQ</h3>
+<p>Below are the frequently asked questions. If you have a question not on this list, please let me know!</p>
+<ol>
+  <li class="dcount"> I have installed everything according to this document, but when I run the agent, I get an error stating:<br/>
+    <br/>
+    <pre class=script>
+    "An empty value was found where a yes or no was expected in the config file ..."</pre>
+    <p>What did I do wrong?</p>
+    <p><strong>A.</strong><br/>First, please ensure that all of the values are filled out properly. If that wasn't the problem, then try adding the following line to the bottom of the config file:</p>
+    <pre class=script>    agent.output.flatfile = yes </pre>
+    <p>Once you have added that value to the config file, try testing the agent again.</p>
+  </li>
+</ol>
 <hr>
 <div align=right class="address">
   <address>
@@ -480,6 +495,7 @@
   <!-- hhmts start -->
   Last modified: Tue May 17 15:49:04 2005
   <!-- hhmts end -->
+  <p>$Date$</p>
 </div>
 </body>
 </html>