[MOBY-guts] biomoby commit

[Eddie Kawas]

kawas
Mon Oct  1 15:05:38 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv13606

Modified Files:
	InstallingLocalMOBYCentral.html 
Log Message:
mention that MOBY_ONTOLOGYSERVER needs to be added to the environment and added it in the appropriate spots during installation
moby-live/Docs/MOBY-S_API InstallingLocalMOBYCentral.html,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html	2007/02/22 16:22:24	1.8
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html	2007/10/01 19:05:38	1.9
@@ -154,6 +154,10 @@
         # from the mobycentral databases.
         #
         SetEnv MOBY_CENTRAL_CONFIG "/etc/apache2/conf/mobycentral.config"
+        # Full URL to the <a href="#ONTOLOGYSERVER">OntologyServer.cgi</a> script 
+        # that is copied to the cgi-bin
+        #
+        SetEnv MOBY_ONTOLOGY_SERVER "http://<i>your.domain</i>/cgi-bin/OntologyServer.cgi"
         # 
         # Path to additional Perl modules.
         # Tell Apache where to find Perl modules,
@@ -460,11 +464,6 @@
      <li>Copy the 
       <pre>    ~/moby-live/Perl/scripts/OntologyServer.cgi </pre>
          CGI script into your webserver cgi-bin folder.     </li>
-     <li>You will now have to edit the MOBY::Client::OntologyServer.pm module manually (sorry!). 
-         This module was hardcoded to point to the OntologyServer.cgi at THE central BioMOBY Central.  
-         You will have to change the line that reads 
-      <pre>    host => ["http://mobycentral.icapture.ubc.ca/cgi-bin/OntologyServer.cgi",'read/write'] </pre>
-         to point to the URL of your OntologyServer.cgi that you just set up.     </li>
 	</ul>
    </li>
    <!--
@@ -545,12 +544,16 @@
          then set up the following environment variables. <br/>
          For bash, ksh, etc. in your ~/.bashrc or ~/.kshrc or etc.: 
        <pre>
-    export MOBY_SERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
-    export MOBY_URI=http://<i>your.host.name</i>t/MOBY/Central </pre>
+export MOBY_SERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
+export MOBY_URI=http://<i>your.host.name</i>t/MOBY/Central
+export MOBY_ONTOLOGYSERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/OntologyServer.cgi
+	   </pre>
          For csh or tcsh in your ~/.cshrc or ~/.tcshrc: <br/> 
        <pre>
-    setenv MOBY_SERVER http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
-    setenv MOBY_URI http://<i>your.host.name</i>/MOBY/Central </pre>
+setenv MOBY_SERVER http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
+setenv MOBY_URI http://<i>your.host.name</i>/MOBY/Central
+setenv MOBY_ONTOLOGYSERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/OntologyServer.cgi
+	   </pre>
      </li>
     </ul>
    </li>
@@ -563,7 +566,8 @@
    <b>To test your BioMOBY Central:</b>
    <ul>
     <li>Ensure that the following environment variables are set:
-      <pre>    MOBY_CENTRAL_CONFIG - the path to your <a href="#mobycentral.config">mobycentral.config file</a> created above </pre>
+      <pre>    MOBY_CENTRAL_CONFIG - the path to your <a href="#mobycentral.config">mobycentral.config file</a> created above</pre>
+	  <pre>    MOBY_ONTOLOGYSERVER - the url to your <a href="#ONTOLOGYSERVER">OntologyServer.cgi file</a> created above</pre>
       <pre>    MOBY_SERVER - the endpoint of your local registry (see above, <a href="#CLIENTS">Configure your clients</a>)</pre>
       <pre>    MOBY_URI - the namespace of your local registry (see above, <a href="#CLIENTS">Configure your clients</a>)</pre>
     </li>