Re: [Opaltoolkit-users] Opal 2.4 and Tomcat

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Opal is now working fine for me with tomcat6 when I run it on a single 
host.  My next step is to turn it into a cluster service (Redhat 
Enterprise Linux 6 clustering).  Using the exact same Opal configuration 
except changing:
     tomcat.url=http://crick.cgl.ucsf.edu:8080
to
     tomcat.url=http://webservices.rbvi.ucsf.edu
in etc/opal.properties, I get the error message in the attached 
catalina.out file.

It appears to be a permissions problem, and I have a guess at what it 
might be.  webservices.rbvi.ucsf.edu:80 is actually an Apache instance 
configured to forward requests to opal2/* to tomcat.  I'm guessing that 
somehow the opal/tomcat instance can tell whether the deployment request 
came from itself.  In the crick:8080 case, it did, and everything 
worked; in the webservices:80 case, it did not, and resulted in the 
rejection.  What I do not know is where this permission check occurs (in 
tomcat or opal).  A couple hours of research suggested that I need to have a
     <Valve className="org.apache.catalina.valves.RemoteAddrValve" ...
statement somewhere, but I really do not know tomcat or opal well enough 
to figure it out.

Any suggestions?

Thanks.

Conrad

On 1/10/2014 12:47 PM, Conrad Huang wrote:
> Ah, that was just stupidity on my part.  I moved tomcat6 and forgot to
> update hibernate-opal.cfg.xml.  Sorry about the silly question.
>
> Conrad
>
> On 1/10/2014 12:34 PM, Luca Clementi wrote:
>> 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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>>>
>
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