From Sukdith.Punjasthitkul at dartmouth.edu Wed Apr 1 02:32:08 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Wed, 1 Apr 2015 06:32:08 +0000 Subject: [Eagle-i-admins] [ eagle-i-admins ] Broken link in SWEET when upgrading to 3.4.2, public sparqler issues In-Reply-To: References: <2E9996F4-D9B1-4343-874F-9B7D6DB180D4@dartmouth.edu> Message-ID: 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 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 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-- >> >> >> >> >> >> >> >> > From Sophia_Cheng at hms.harvard.edu Wed Apr 1 10:25:20 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Wed, 1 Apr 2015 10:25:20 -0400 Subject: [Eagle-i-admins] [ eagle-i-admins ] Broken link in SWEET when upgrading to 3.4.2, public sparqler issues In-Reply-To: References: <2E9996F4-D9B1-4343-874F-9B7D6DB180D4@dartmouth.edu> Message-ID: 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 > 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 > 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 > 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-- -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sophia_Cheng at hms.harvard.edu Wed Apr 1 13:13:57 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Wed, 1 Apr 2015 13:13:57 -0400 Subject: [Eagle-i-admins] Updates to release notes for version 3.3.0 & 3.4.2 Message-ID: Hello there, We realized that some information was missing from our release notes. They are now updated (https://open.med.harvard.edu/wiki/display/eaglei/3.3.0+Release+Notes and https://open.med.harvard.edu/wiki/display/eaglei/3.4.2+Release+Notes+(Current+Release)) The updates include: * Backward compatibility issue with node-registry.xml file * Requirement of public SPARQLer version 2.0MS3.07 and later * implications of not having a newer version Apologies if any confusion was caused because of these omissions. Thank you. Cheerios, Sophia ---- Sophia K. Cheng Technical Lead Harvard Catalyst | eagle-i email: sophia?_cheng at hms.harvard.edu skype: sophia.k.cheng web: www. eagle-I.net Harvard Medical School Harvard Catalyst | The Harvard Clinical and Translational Science Center Landmark Center, Suite 504 West 401 Park Drive Boston, MA 02215 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sukdith.Punjasthitkul at dartmouth.edu Thu Apr 2 15:29:14 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Thu, 2 Apr 2015 19:29:14 +0000 Subject: [Eagle-i-admins] [ eagle-i-admins ] Broken link in SWEET when upgrading to 3.4.2, public sparqler issues In-Reply-To: References: <2E9996F4-D9B1-4343-874F-9B7D6DB180D4@dartmouth.edu> Message-ID: <51CE0BF9-2493-46D4-9D1F-90823DEE4B84@dartmouth.edu> 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 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 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 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 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-- >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >> > > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins From fcoldren at mail.med.upenn.edu Thu Apr 30 15:59:36 2015 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Thu, 30 Apr 2015 15:59:36 -0400 Subject: [Eagle-i-admins] output of make-snapshot.sh Message-ID: Hi, We saw that the users.trig file output by make-snapshot.sh stores the credentials in plain text. Is this by design? If so, is there a plan to change the output of user credentials to a hash? Thank you, Faith -------------- next part -------------- An HTML attachment was scrubbed... URL: