Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

[Luca C. <luc...@gm...>]

On Wed, Jan 8, 2014 at 7:39 PM, Conrad Huang <co...@cg...> wrote:
> 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.

My bad. Sorry for not checking the code before answering.
The version was not updated in web.xml.
It's fixed now in the code (I just pushed it).

>>> 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)

This is really weird.
It seems that the user the tomcat container is running under does not
have listing permission on the deploy directory.
Can you verify that?

The code looks ok to me:
            logger.info("initDeployServlet: deploy path: " + deployPathFile );
            [...]
            File [] deployFileList = deployPathFile.listFiles();
            for (File configFile : deployFileList){

listFile() returns null only if the deployPathFile is non existent.

Sincerely,
Luca