Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

[Conrad H. <co...@cg...>]

On 1/8/2014 4:34 PM, Luca Clementi wrote:
> Hey Conrad,
> I'm re-adding the list...
>
> On Wed, Jan 8, 2014 at 2:10 PM, Conrad Huang <co...@cg...> wrote:
>> We're close, but not quite there yet.  I got an instance of Opal 2.5 running
>> under Tomcat6 by simply following the instructions.  I can reach the
>> dashboard.  That's the good news.  The bad news are:
>>
>> 1. The "Server Info" tab says I'm still running Opal version 2.4.
>
> You must have copied you old build.properties from the previous installation.
> The template in the repo seems correct:
> https://github.com/nbcrrolls/opaltoolkit/blob/master/opal/opal2-core/build.properties.template
>
> Can you try to re-deploy upgrading the version number in it (as in the
> template)?

I removed everything and started over, but the results are still the 
same: "Opal Version: 	2.4" in the Server Info tab.  I'm not using any 
configuration files from our production system.  All the .property files 
copied from the .template files and the only changes made are 
catalina.home in build.properties and tomcat.url in opal.properties.

build.properties has "version = 2.5" in it.  In fact, since I've never 
actually installed Opal 2.4, I cannot even imagine where the dashboard 
is finding that version number.  Our current production version is 2.2.

I've been cleaning up the Opal source tree with "ant clean".  Is that 
the proper command?  As for tomcat, I actually delete the directory and 
recopy everything when I start over from scratch.

>> 2. When I first tried to deploy an application (I copied the
>> clustalw_config.xml file and changed the binary path), I got:
>>
>
> No, the new opal has a new deployment method.
> No need to run any command, just drop the file inside $CATALINA_HOME/deploy.
> To undeply rm the file from the folder.
> This is one of the new feature of opal 2.5.
>
> See the docs in dockboot (I know it is not very readable :-():
> https://github.com/nbcrrolls/opaltoolkit/blob/master/opal/opal2-core/docbook/serversetup.sgml#L314
>
> In particular:
> <para>Deploy the services inside Tomcat, by copying the
> <emphasis>date.xml</emphasis> file inside the
> directory specified in
> <emphasis>$OPAL_HOME/etc/opal.properties</emphasis> with the keyword
> <emphasis>opal.deploy.path</emphasis>.
> If you have not changed this property the default directory is
> <emphasis>$CATALINA_HOME/deploy</emphasis>.
> <screen>
>      cp configs/date.xml $CATALINA_HOME/deploy
> </screen>
> </para>

I missed that one.  Now, in opal.properties, I have:
	opal.deploy.path=deploy
My CATALINA_HOME is /usr/local/opal-tomcat6 and I copied 
clustalw_config.xml to /usr/local/opal-tomcat6/deploy.  Going to the 
dashboard, I do not see the service.  However, I did see in 
$CATALINA_HOME/logs/catalina.out the following:

> Jan 8, 2014 7:19:34 PM org.apache.catalina.startup.Catalina start
> INFO: Server startup in 2500 ms
> 2014-01-08 19:19:36,967 INFO  edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer
> .run(OpalDeployService.java:160) - initDeployServlet: axis URL: http://crick.cgl
> .ucsf.edu:8080/opal2/servlet/AxisServlet
> 2014-01-08 19:19:36,968 INFO  edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer
> .run(OpalDeployService.java:161) - initDeployServlet: deploy path: deploy
> Exception in thread "OpalDeployer" java.lang.NullPointerException
>         at edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployServ
> ice.java:177)

>
> Luca
>

Conrad