[MOBY-guts] biomoby commit

Eddie Kawas kawas at dev.open-bio.org
Wed Oct 11 20:39:32 UTC 2006


kawas
Wed Oct 11 16:39:31 EDT 2006
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv27923/Java/docs

Modified Files:
	RegistryServlets.html 
Log Message:
Added some configuration information.

moby-live/Java/docs RegistryServlets.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/RegistryServlets.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/RegistryServlets.html	2006/10/10 18:51:50	1.1
+++ /home/repository/moby/moby-live/Java/docs/RegistryServlets.html	2006/10/11 20:39:31	1.2
@@ -4,6 +4,11 @@
 <link rel="stylesheet" href="images/stylesheet.css" type="text/css">
 <link rel="shortcut icon" href="images/whale.gif">
 <title>Registry Servlets</title>
+<style type="text/css">
+<!--
+.mail {font-size: medium}
+-->
+</style>
 </head>
 <body>
 <h1>BioMOBY Registry Servlets</h1>
@@ -15,7 +20,7 @@
     <li class="dcount">Types 'script' - a servlet that is used to generate textual dumps for the Object, Namespace and Service Type ontologies.</li>
     <li class="dcount">LSID Authority Servlet -  a servlet that is used to resolve <em>biomoby.org</em>*, LSIDs to metadata.</li>
     <li class="dcount">Service Tester Servlet - a servlet that periodically 'pings' the services contained in the registry to determine whether or not the services URL are resolvable.</li>
-    <li class="dcount">RDFAgent Validator - a servlet that can be used to test whether your installation of the agent was successful, or to test an RDF document that describes your services for syntatical errors.</li>
+    <li class="dcount">RDFAgent Validator - a servlet that can be used to test whether your installation of the agent was successful, or to test an RDF document that describes your services for syntactical errors.</li>
     <li class="dcount">LSID client web applications that can be used to resolve LSIDs. One of these applications uses AJAX and provides auto complete functionality. </li>
   </ol>
 </ol>
@@ -41,8 +46,13 @@
 <h1>Installing the Servlets</h1>
 <p class="indent">Installing the servlets is extremely straight-forward and quite easy.</p>
 <ol>
-  <li class="dcount">Download the installation file from ...</li>
-  <li class="dcount">Run the installer, making sure to follow the on screen prompts. </li>
+  <li class="dcount">Download the installation file from <a href="http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar">http://bioinfo.icapture.ubc.ca/ekawas/servlets/install.jar</a> <br>
+    <br>
+  </li>
+  <li class="dcount">From the command line, enter the following command <br/>
+    <pre class="script">java -jar install.jar</pre>
+    <p>A GUI should result that will guide you through the installation process. </p>
+  </li>
   <li class="dcount">Your done! Now all you have to do is configure your newly installed servlets. </li>
 </ol>
 <a name="config"></a>
@@ -55,7 +65,15 @@
       <li>The exact location of the mobycentral.config (confused? refer <a href="http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html#MYSQL" target="_blank">here</a>) </li>
       <li>Your JAVA J2EE servers complete address</li>
     </ul>
-    <p>Once you have those values, you will have to modify the servlets configuration file that is located at <b class="step">/path/to/tomcat/webapps/authority/META-INF/context.xml</b> </p>
+    <blockquote>
+      <p><b class="subtitle">How to Configure</b> </p>
+      <ul>
+        <li><a href="#context">context.xml</a></li>
+        <li><a href="#mobycentral">mobycentral.config</a></li>
+        <li><a href="#DNS">DNS records &amp; Apache (If you wish to use the LSID authority servlet).</a> </li>
+      </ul>
+    </blockquote>
+    <p class="subtitle"><a name="context"></a>Once you have those values, you will have to modify the servlets configuration file that is located at <b class="step">/path/to/tomcat/webapps/authority/META-INF/context.xml</b> </p>
     <p>The file <b class="step">context.xml</b> is written in XML and contains numerous entries that look like this: </p>
     <pre class="script">
 	
@@ -115,12 +133,14 @@
         <td width="25%" align="center" class="text">suffix</td>
         <td width="75%" align="left" class="text">The file name suffix </td>
       </tr>
-      <tr>
-        <td width="100%" class="text"><span class="note">For a more precise explanation of how to configure this aspect of the servlets, please refer to <a href="http://tomcat.apache.org/tomcat-5.5-doc/config/valve.html" target="_blank">http://tomcat.apache.org/tomcat-5.5-doc/config/valve.html</a></span></td>
-      </tr>
     </table>
+    <blockquote>
+      <blockquote>
+        <p><span class="note">For a more precise explanation of how to configure this aspect of the servlets, please refer to<br/> <a href="http://tomcat.apache.org/tomcat-5.5-doc/config/valve.html" target="_blank">http://tomcat.apache.org/tomcat-5.5-doc/config/valve.html</a></span></p>
+      </blockquote>
+    </blockquote>
     <p>Once you have modified these parameters in this file, you may close the file.</p>
-    <p>Next, you will have to open the file <b class="step">mobycentral.config</b> and add or modify a couple of configuration parameters:</p>
+    <p class="subtitle"><a name="mobycentral"></a>Next, you will have to open the file <b class="step">mobycentral.config</b> and add or modify a couple of configuration parameters:</p>
     <li>To the<b class="update"> [mobycentral] </b>section of this file, please ensure that the following parameters are set: </li>
     <table width="65%" border="1" align="center">
       <tr>
@@ -164,7 +184,7 @@
       </tr>
     </table>
     <p>&nbsp;</p>
-	<li>To the<b class="update"> [mobynamespace] </b>section of this file, please ensure that the following parameters are set: </li>
+    <li>To the<b class="update"> [mobynamespace] </b>section of this file, please ensure that the following parameters are set: </li>
     <table width="65%" border="1" align="center">
       <tr>
         <td width="25%" align="center" class="text">lsid_authority</td>
@@ -183,7 +203,7 @@
       </tr>
     </table>
     <p>&nbsp;</p>
-	<li>To the<b class="update"> [mobyservice] </b>section of this file, please ensure that the following parameters are set: </li>
+    <li>To the<b class="update"> [mobyservice] </b>section of this file, please ensure that the following parameters are set: </li>
     <table width="65%" border="1" align="center">
       <tr>
         <td width="25%" align="center" class="text">lsid_authority</td>
@@ -201,16 +221,50 @@
           <p> This value is most likely: http://yourDomain:yourPort/authority/RESOURCES/MOBY-S/ServiceTypes </p></td>
       </tr>
     </table>
-    <p>Once these values have been added or modified, make sure to save the configuration files and restart the server. Your changes should be reflected in your registry. </p>
+    <p>&nbsp;</p>
+    <p class="subtitle"><a name="dns"></a>To enable the LSID authority servlets, you will have to perform up to 2 more tasks:</p>
+    <ul>
+      <li>Create a DNS record for your domain</li>
+      <li>Add ProxyPass directives to your Apache servers' configuration file <em>(optional)</em> </li>
+    </ul>
+    <p><strong>Setting up DNS</strong> (<a href="http://www-128.ibm.com/developerworks/opensource/library/os-lsid/#N10560" target="_blank">excerpt</a>) </p>
+    <blockquote>
+      <p>All that you - or your system administrator - must do, is to add a service record for the machine that will run the authority. </p>
+      <p>Suppose the machine is authority.company.net and that it will serve as the authority named company.net. Further suppose that the service will be on port 8080. The record that must be added should go into the master zone file for company.net's DNS server (perhaps a file named /var/named/company.net.zone on company.net):</p>
+      <pre class="script">_lsid._tcp      IN      SRV     1       0       8080    authority.company.net.</pre>
+      <p>If the authority name is supposed to be authority.company.net rather than company.net, the record in company.net's zone file should look like:</p>
+      <pre class="script">_lsid._tcp.authority    IN      SRV     1       0       8080    authority.company.net. </pre>
+    </blockquote>
   </ul>
+  <blockquote>
+    <p><strong>Enabling ProxyPass Apache Directives</strong></p>
+    <blockquote>
+      <p>For those of you that are running Tomcat on a non-standard port, you may find that users of your registry cannot access those ports due to firewall restrictions. One way around this is to set up ProxyPass directives in your web server.</p>
+      <p><b class="sb">Before you begin, it is highly recommended that you backup any files mentioned here that you will be updating. </b></p>
+      <p>Open up your Apache servers httpd.conf file and make sure that following line is uncommented:</p>
+      <pre class="script">LoadModule proxy_module modules/mod_proxy.so </pre>
+      <p>Then add the following to the bottom of the file</p>
+      <pre class="script">
+ProxyPass /authority http://localhost:8080/authority
+ProxyPass /authority/ http://localhost:8080/authority/
+ProxyPass authority http://localhost:8080/authority
+ProxyPass authority/ http://localhost:8080/authority/ </pre>
+      Now requests made to <em><strong>localhost/authority</strong></em> will be sent to <em><strong>localhost:8080/authority</strong></em> and your users should not have any problems accessing the URLs. </blockquote>
+  </blockquote>
+  <p>Once these values have been added or modified, make sure to save the configuration files and restart the server. Your changes should be reflected in your registry. </p>
 </ul>
 <a name="testing"></a>
 <h1>Testing Your Servlets</h1>
-<p class="indent"> </p>
+<p class="indent">Once you have installed and configured the servlets, you can determine if the install was successful by attempting to resolve the following URL:</p>
+<blockquote>
+  <p class="indent">http://<em><strong>your.domain.com</strong></em>:<strong><em>your_port</em></strong>/authority/moby.jsp</p>
+</blockquote>
+<p class="indent">where <em><strong>your.domain.com</strong></em> is the domain name of the server that the servlets were installed on and <em><strong>your_port</strong></em> is the server port. </p>
+<p class="indent">The resulting page will outline those servlets that are included in this distribution and will provide you with links to test them. </p>
 <hr>
 <div align=right class="address">
   <address>
-  <A HREF="mailto:ekawas at mrl.ubc.ca">Edward A Kawas</A><BR>
+  <A HREF="mailto:ekawas at mrl.ubc.ca" class="mail">Edward A Kawas</A><BR>
   </address>
   <!-- hhmts start -->
   <!-- hhmts end -->




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