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

[Sukdith Punjasthitkul]

Hi Sophia, 

I've re-installed sparqler from scratch, also making sure to remove eaglei.sparqler.lastSynchronizedDateFile from eagle-i-apps.properties and eagle-i-sparqler.last-sync-date.properties file from [eagle-i home]/conf directory.

In the repository.log, I see

2015-04-02 04:39:47,705 T=SpqlrSyncTmr INFO org.eaglei.repository.sparqler.SyncTimer$SyncTimerTask - Harvest to Synchronizer succeeded.

so I think the public SPARQLer is now working as expected. 


Thank you for your help with this!

--sukie--





> On Apr 1, 2015, at 10:25 AM, Cheng, Sophia <Sophia_Cheng at hms.harvard.edu> wrote:
> 
> 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> 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> 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> 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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