[Eagle-i-admins] [ eagle-i-admins ] Broken link in SWEET when upgrading to 3.4.2, public sparqler issues

[Cheng, Sophia]

Hi Sukie,

That’s odd. I suggest then to remove all traces of your existing sparqler:

- [eagle-i-home]/eaglei/sparqler
- tomcat/webapps/sparqler

And then try installing the sparqler from scratch.

As of version 3.1.1 (https://open.med.harvard.edu/wiki/display/eaglei/3.1.1+Release+Notes#id-3.1.1ReleaseNotes-SPARQLer), we’ve simplified the sparqler a little bit by removing the use of the timestamp file. We are now maintaining the last synchronized time in memory.

Could you give that a try?

Thanks,
Sophia

On Apr 1, 2015, at 2:32 AM, Sukdith Punjasthitkul <Sukdith.Punjasthitkul at dartmouth.edu<mailto:Sukdith.Punjasthitkul at dartmouth.edu>> wrote:

Hi Sophia,

RE: ontology browser link fix, sounds good.

RE: SPARQLer, we're not running a cron job for SPARQL endpoint. My understanding was that an update summary was outputted to eagle-i-sparqler.last-sync-date.properties, which is currently not the case. Also, I've been unsuccessful in performing a manual synchronization using synchronize-sparqler.sh.

--sukie--



On Mar 31, 2015, at 12:09 PM, Cheng, Sophia <Sophia_Cheng at hms.harvard.edu<mailto:Sophia_Cheng at hms.harvard.edu>> wrote:

Hi Sukie,

We are aware of the broken ontology browser link.  That is currently being fixed.  When it is, a restart of the node should pull in the correct link information. We’ll let you know when that’s ready.

Regarding the public sparqler, we think you may have an out dated cron job hanging around. In a much earlier iteration of the public SPARQL endpoint, the installation instructions included setting up a crontab to perform the synchronization.  We no longer need this, the synchronization is now handled by the public SPARQLer itself.  (Old documentation here: https://open.med.harvard.edu/wiki/pages/viewpage.action?pageId=10190875)

Removing the cron job and then restarting should do the trick.

Let us know if that isn’t the case.

Thanks!
-Sophia


On Mar 31, 2015, at 10:34 AM, Sukdith Punjasthitkul <Sukdith.Punjasthitkul at dartmouth.edu<mailto:Sukdith.Punjasthitkul at dartmouth.edu>> wrote:

We just updated to version 3.4.2 and noticed that in SWEET, the Ontology Browser link is broken.
It currently points to:

https://dartmouth.eagle-i.net:8443/sweet/default_value/model/

I'm getting a 404 Error: "The requested resource (/sweet/default_value/model/) is not available."

We are also running into issues trying to synchronize the public sparqler. Running synchronize-sparqler.sh resulted in the following error:

Error: Main method not found in class org.eaglei.repository.sparqler.SynchronizerCommand, please define the main method as:
 public static void main(String[] args)

I updated the sparqler by turning off Tomcat, deleting the .war and sparqler/ file from $CATALINA_HOME/webapps/, copying over sparqler.war file from repo/webapps/, and then starting Tomcat up. I did not recreate the Sparqler admin or finish-install steps. Does updating sparqler require rebuilding the repo users as well?

--sukie--











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