Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

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

On Fri, Jan 10, 2014 at 12:08 PM, Conrad Huang <co...@cg...> wrote:
> Hi, Luca.  Sorry to reopen the thread, but...
>
> Just to make sure I can reproduce things, I removed everything and started
> over.  I changed the tomcat startup script so that tomcat starts in
> $CATALINA_HOME.  I reset opal.deploy.path back to simply "deploy" instead of
> the absolute path.  I copied the tomcat6 files and reinstalled Opal 2.5.
> Unfortunately, when I start tomcat, I'm getting these strange database
> timeouts again.  I've attached logs/catalina.out.
>
> The Opal server does eventually serve up pages.  Service deployment works
> (copying file to "deploy" directory makes it show up in dashboard "List of
> Application").  Clicking on the dashboard Statistics tab does not work and
> generates the errors towards the end of catalina.out.
>
> Any suggestions?  Thanks.


What kind of database are you using?
The problem is probably located in your hibernate file:
etc/hibernate-opal.cfg.xml

You have a communication problem (if you use hsql tomcat probably you
can't write to the file in connection.url:
<property name="connection.url">jdbc:hsqldb:file:/home/clem/projects/opaltoolkit/apache-tomcat-7.0.27/webapps/opal2/WEB-INF/data/opaldb</property>)


Luca



> On 1/9/2014 2:36 PM, Conrad Huang wrote:
>>
>> On 1/9/2014 2:22 PM, Luca Clementi wrote:
>>>
>>> On Thu, Jan 9, 2014 at 1:45 PM, Conrad Huang <co...@cg...> wrote:
>>>>
>>>> On 1/9/2014 11:35 AM, Luca Clementi wrote:
>>>>>
>>>>>
>>> [...]
>>>>
>>>> The debug code clears it up a bit.  Here's the end of catalina.out
>>>> (adding
>>>> debugging code but leaving deploy as "deploy"):
>>>>
>>>>> INFO: Server startup in 2609 ms
>>>>> 2014-01-09 13:28:08,074 INFO
>>>>>
>>>>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployService.java:160)
>>>>> - initDeployServlet: axis URL:
>>>>> http://xxx.xxx.ucsf.edu:8080/opal2/servlet/AxisServlet
>>>>> 2014-01-09 13:28:08,075 INFO
>>>>>
>>>>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployService.java:161)
>>>>> - initDeployServlet: deploy path: deploy
>>>>> 2014-01-09 13:28:08,075 INFO
>>>>>
>>>>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployService.java:162)
>>>>> - initDeployServlet: deploy path: /var/www/deploy
>>>>>
>>>>> Exception in thread "OpalDeployer" java.lang.NullPointerException
>>>>>           at
>>>>>
>>>>> edu.sdsc.nbcr.opal.util.OpalDeployService$Deployer.run(OpalDeployService.java:178)
>>>>
>>>>
>>>>
>>>> The full deploy path is relative to /var/www, which is the home
>>>> directory of
>>>> user "apache" which is the account we use for running this instance of
>>>> tomcat.  I guess tomcat6 does not change directory from where it was
>>>> started
>>>> to $CATALINA_HOME.  Our startup script uses "su - apache -c ..." to
>>>> start
>>>> tomcat, so it starts in ~apache or /var/www. Specifying the full path in
>>>> etc/opal.properties makes everything work. I have one service deployed!
>>>>
>>>
>>> That does not make much sense to me :-(
>>> It should not use the current working directory (that was my first test).
>>> What script do you use to start up tomcat?
>>> You should use the $CATALINA_HOME/bin/startup.sh which sets the proper
>>> working directory:
>>> clem@hermes:~/projects/opaltoolkit$ apache-tomcat-6.0.37/bin/startup.sh
>>> Using CATALINA_BASE:
>>> /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37
>>> Using CATALINA_HOME:
>>> /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37
>>> Using CATALINA_TMPDIR:
>>> /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37/temp
>>> Using JRE_HOME:        /usr
>>> Using CLASSPATH:
>>> /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37/bin/bootstrap.jar
>>>
>>> No matter where I start it from....
>>> I tried to reproduce your problem but still no luck
>>> cd /tmp
>>> su - clem -c
>>> /home/clem/projects/opaltoolkit/apache-tomcat-6.0.37/bin/startup.sh
>>>
>>>
>>> Luca
>>>
>>
>> We're on Redhat Enterprise Linux 6.  There is no startup.sh in
>> /usr/share/tomcat6/bin.  I copied the startup file from
>> /etc/init.d/tomcat6.  In that script it invokes /usr/sbin/tomcat6, which
>> ultimately runs java with no intervening chdir:
>>
>> /usr/lib/jvm/java/bin/java
>>
>> -Djavax.sql.DataSource.Factory=org.apache.commons.dbcp.BasicDataSourceFactory
>> -classpath
>>
>> :/usr/local/opal-tomcat6/bin/bootstrap.jar:/usr/local/opal-tomcat6/bin/tomcat-juli.jar:/usr/share/java/commons-daemon.jar
>> -Dcatalina.base=/usr/local/opal-tomcat6
>> -Dcatalina.home=/usr/local/opal-tomcat6 -Djava.endorsed.dirs=
>> -Djava.io.tmpdir=/usr/local/opal-tomcat6/temp
>>
>> -Djava.util.logging.config.file=/usr/local/opal-tomcat6/conf/logging.properties
>> -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
>> org.apache.catalina.startup.Bootstrap start
>>
>> Conrad
>>
>>
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