SDS:Feb 9-13 2009 VSTO Replica Meeting

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VSTO replica

Action Items:

  • (DONE) Josh will move the installs of tomcat, pellet, maven, etc to /opt
  • Cynthia will configure tomcat to use jsvc to run as the tomcat user and the apache connector
  • (DONE)Josh will install TCPFlow to determine what is being sent.
  • Will we install multiple tomcats or do we modify the VSTO portal code so that multiple applications can run on the same installation. Could also run multiple instances from the same installation using different port and configuration?
  • Josh will check on the database connection, sending of username and password.
  • Cynthia will install startup script for tomcat
  • Cynthia will install a startup script for pellet
  • (DONE)Peter is getting vsto.rpi.edu.
  • Stephan will edit httpd.conf to get vsto.rpi.edu
  • Patrick will take a look at turning off authentication with Acegi for now until we can get the authentication piece resolved.
  • Stephan will create documentation for how to install and run the replica portal
    • VSTO Replica Portal Page
    • software installed and versions
    • software dependencies
    • configuration (include jsvc, apache connector)
  • Patrick will look in to the ip issue with dataportal/cedarweb/proxy (related to problem Josh is having with connection hanging (below))

Next status meeting

  • 2pm ET, noon MT, 11PT

Current Status:

  • VSTO is installed but it is not working

From Josh: 

I've spent some time today trying to get the VSTO webapp up and running on escience, but so far without success.
The webapp hangs in the VSTOservice init method, like so:

[...]
  - locked <0x00002aab5c09b960> (a sun.net.www.protocol.http.HttpURLConnection)
  at edu.stanford.smi.protegex.owl.inference.dig.reasoner.DefaultDIGReasoner.performRequest(DefaultDIGReasoner.java:206)
  at edu.stanford.smi.protegex.owl.inference.dig.reasoner.DefaultDIGReasoner.getIdentity(DefaultDIGReasoner.java:125)
  at edu.stanford.smi.protegex.owl.inference.protegeowl.DefaultProtegeOWLReasoner.isConnected(DefaultProtegeOWLReasoner.java:288)
  at ncar.vsto.VSTOservice.init(Unknown Source)
[...]

...apparently waiting for an HTTP connection to close.  I tried two versions of Tomcat, three versions of Pellet
on the server before realizing that the webapp also hangs in the same way on my local machine, whereas it never did
so before.  That makes me wonder whether DefaultDIGReasoner is making a call not only to the Pellet service but also
to an external web service which happens to be down.  That would be strange, but I haven't found the right revision of
the protege-owl source code in order to figure out what's really going on.  Those I've looked at so far don't agree with
the stack trace, and the VSTO source code gives no indication of which version of protege-owl.jar we're dealing with
(note: another advantage of Maven over Ant is that the POM contains versioning information for all dependencies).

From Luca: 

this looks more like a firewall problem to me.... if it was a problem with the versions of protege-owl.jar and protege.jar,
we would probabily see it at NCAR too.

I believe the VSTO web app makes connections to pellet on port 8081, which *might* be blocked at RPI. Pellet, in its turn,
needs access to the ontology on dataportal.ucar.edu.

My suggestion would be to also try to access pellet outside of the vsto code and see if it is succesfull.

Incidentally, I don't know what is exactly the version of protege-owl.jar - the jar MANIFEST doesn't seem to contain that information.
  • Web Services
    • cedar catalog
    • mlso catalog
    • cedar authentication
      • for the short term we could shut this off and use the plotting username, which will give us access to opendap from the replica.
    • change vsto java code to use web services instead of jdbc
    • Josh almost has working Universal SQL Gateway, which on cedarweb would be run as an app under tomcat
      • will need to install Tomcat on butters and Universal SQL Gateway
  • SVN
    • it's installed, about another week before can begin using
  • startup scripts for tomcat and pellet
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