From jlease at hmc.psu.edu Mon Mar 2 15:26:48 2015 From: jlease at hmc.psu.edu (Lease, Joshua) Date: Mon, 2 Mar 2015 20:26:48 +0000 Subject: [Eagle-i-admins] Release Notes Message-ID: Admins, We're looking for release notes or a changelog for the most recently released version of eagle-i. Does anyone know where we can find these documents? Thanks, Joshua Lease From Sophia_Cheng at hms.harvard.edu Tue Mar 3 10:31:42 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Tue, 3 Mar 2015 10:31:42 -0500 Subject: [Eagle-i-admins] Release Notes In-Reply-To: References: Message-ID: Hello Admins, I?m sorry for the delay in getting release notes out. I am hoping to have 3.1.1 notes ready later this evening, tomorrow morning at the latest. The next few release notes (3.2 - 3.3) should be much quicker to turn around. Thank you for your patience. Cheerios, Sophia > On Mar 2, 2015, at 3:26 PM, Lease, Joshua wrote: > > Admins, > > We're looking for release notes or a changelog for the most recently > released version of eagle-i. Does anyone know where we can find these > documents? > > Thanks, > Joshua Lease > > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins From Sukdith.Punjasthitkul at dartmouth.edu Tue Mar 3 10:37:38 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Tue, 3 Mar 2015 15:37:38 +0000 Subject: [Eagle-i-admins] Release Notes In-Reply-To: References:

Message-ID: Hi Sophia, Thank you for the update. We are currently running 3.0.4. Can we update straight to 3.3.0 or do we need to go through each update in order? Thanks, --sukie-- > On Mar 3, 2015, at 10:31 AM, Cheng, Sophia wrote: > > Hello Admins, > > I?m sorry for the delay in getting release notes out. I am hoping to have 3.1.1 notes ready later this evening, tomorrow morning at the latest. The next few release notes (3.2 - 3.3) should be much quicker to turn around. > > Thank you for your patience. > > Cheerios, > Sophia > >> On Mar 2, 2015, at 3:26 PM, Lease, Joshua wrote: >> >> Admins, >> >> We're looking for release notes or a changelog for the most recently >> released version of eagle-i. Does anyone know where we can find these >> documents? >> >> Thanks, >> Joshua Lease >> >> _______________________________________________ >> Eagle-i-admins mailing list >> Eagle-i-admins at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins > > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins From Sophia_Cheng at hms.harvard.edu Tue Mar 3 12:18:33 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Tue, 3 Mar 2015 12:18:33 -0500 Subject: [Eagle-i-admins] Release Notes In-Reply-To: References:

Message-ID: <4857D420-0A34-44C2-AFE0-1F12C51B1AE9@hms.harvard.edu> Hi Sukie, I believe it will be okay to upgrade to 3.3.0, as long as you take into account any property or otherwise breaking changes that occurred in the releases from 3.1.1 - 3.3.0. I can not say for certain if there will be any until I put everything down on ?paper?. I can confidently say that data migration will only need to be run once, as there were no ontology changes since 3.1.1. Does that make sense? Cheerios, Sophia > On Mar 3, 2015, at 10:37 AM, Sukdith Punjasthitkul wrote: > > Hi Sophia, > > Thank you for the update. We are currently running 3.0.4. Can we update straight to 3.3.0 or do we need to go through each update in order? > > Thanks, > > --sukie-- > > > >> On Mar 3, 2015, at 10:31 AM, Cheng, Sophia wrote: >> >> Hello Admins, >> >> I?m sorry for the delay in getting release notes out. I am hoping to have 3.1.1 notes ready later this evening, tomorrow morning at the latest. The next few release notes (3.2 - 3.3) should be much quicker to turn around. >> >> Thank you for your patience. >> >> Cheerios, >> Sophia >> >>> On Mar 2, 2015, at 3:26 PM, Lease, Joshua wrote: >>> >>> Admins, >>> >>> We're looking for release notes or a changelog for the most recently >>> released version of eagle-i. Does anyone know where we can find these >>> documents? >>> >>> Thanks, >>> Joshua Lease >>> >>> _______________________________________________ >>> Eagle-i-admins mailing list >>> Eagle-i-admins at open.med.harvard.edu >>> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins >> >> _______________________________________________ >> Eagle-i-admins mailing list >> Eagle-i-admins at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins > From Sophia_Cheng at hms.harvard.edu Thu Mar 5 13:09:24 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Thu, 5 Mar 2015 13:09:24 -0500 Subject: [Eagle-i-admins] eagle-i version 3.1.1 release Message-ID: Dear eagle-i Sys Admins, We are pleased to announce the release of eagle-i version 3.1.1 (and the accompanying release notes). It is now ready for download. The release notes can be found here: https://open.med.harvard.edu/wiki/display/eaglei/3.1.1+Release+Notes We have changed up how the notes are organized and hope that this new organization helps. This is not the latest and greatest version. We hope to have release notes ready for the subsequent versions by the end of next week. Your patience is greatly appreciated. If you have any questions or comments regarding the documentation, please let us know. Kind Regards, 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 jrobertson3 at hmc.psu.edu Fri Mar 20 13:29:22 2015 From: jrobertson3 at hmc.psu.edu (Robertson, Jim) Date: Fri, 20 Mar 2015 17:29:22 +0000 Subject: [Eagle-i-admins] Broken web links on 3.2.0 Message-ID: We are currently running eagle-i 3.2.0 and have found that several of our previously-working links in the resource footer (e.g. Search Application Help, Getting Started with Search) are now broken. This seems to have happened coincident with the most recent upgrade of eagle-i on the central Consortium site. Can the link destinations be restored for sites running older versions? Regards, Jim Robertson Systems Analyst - Research Informatics Phone: (717) 531-0003 x289483 Email: jrobertson3 at hmc.psu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sophia_Cheng at hms.harvard.edu Sat Mar 21 15:06:58 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Sat, 21 Mar 2015 15:06:58 -0400 Subject: [Eagle-i-admins] Broken web links on 3.2.0 In-Reply-To: References: Message-ID: <58E90417-38C6-44F2-9767-B54B3ADB5D47@hms.harvard.edu> Hi Jim, Sorry about that. We?re going through a revamp of our look and the location of those links got shuffled around. We?ll get those links back for the time being, while the release notes with what the new values should be for those navigation links. We should hopefully have those back sometime on Monday. Thanks, 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 On Mar 20, 2015, at 1:29 PM, Robertson, Jim > wrote: We are currently running eagle-i 3.2.0 and have found that several of our previously-working links in the resource footer (e.g. Search Application Help, Getting Started with Search) are now broken. This seems to have happened coincident with the most recent upgrade of eagle-i on the central Consortium site. Can the link destinations be restored for sites running older versions? Regards, Jim Robertson Systems Analyst ? Research Informatics Phone: (717) 531-0003 x289483 Email: jrobertson3 at hmc.psu.edu _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins -------------- next part -------------- An HTML attachment was scrubbed... URL: From jrobertson3 at hmc.psu.edu Wed Mar 25 08:21:31 2015 From: jrobertson3 at hmc.psu.edu (Robertson, Jim) Date: Wed, 25 Mar 2015 12:21:31 +0000 Subject: [Eagle-i-admins] Missing Browse button on home page for version 3.2.0 Message-ID: All, We are currently on 3.2.0 and noticed that the browse button is missing from the home page (it does still appear on other pages). Was this a side effect of the 3.4 upgrade to the central site? Home page: [cid:image005.jpg at 01D066D4.B2C6FE70] Results page: [cid:image006.jpg at 01D066D4.B2C6FE70] Regards, Jim Robertson Systems Analyst - Research Informatics Phone: (717) 531-0003 x289483 Email: jrobertson3 at hmc.psu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image005.jpg Type: image/jpeg Size: 3597 bytes Desc: image005.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image006.jpg Type: image/jpeg Size: 4685 bytes Desc: image006.jpg URL: From Sophia_Cheng at hms.harvard.edu Wed Mar 25 10:49:30 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Wed, 25 Mar 2015 10:49:30 -0400 Subject: [Eagle-i-admins] Missing Browse button on home page for version 3.2.0 In-Reply-To: References: Message-ID: Hi there all, Sorry, this is another side effect that has occurred with our new look and feel. I will hop on those release notes ASAP and send those around today. Thanks, Sophia On Mar 25, 2015, at 8:21 AM, Robertson, Jim > wrote: All, We are currently on 3.2.0 and noticed that the browse button is missing from the home page (it does still appear on other pages). Was this a side effect of the 3.4 upgrade to the central site? Home page: Results page: Regards, Jim Robertson Systems Analyst ? Research Informatics Phone: (717) 531-0003 x289483 Email: jrobertson3 at hmc.psu.edu _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sophia_Cheng at hms.harvard.edu Thu Mar 26 18:27:07 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Thu, 26 Mar 2015 18:27:07 -0400 Subject: [Eagle-i-admins] eagle-i version 3.4.2 released & other release notes Message-ID: <6BEFC40F-4652-4D53-9015-AD9FC507840D@hms.harvard.edu> Dear eagle-i Sys Admins, We are pleased to announce the release of eagle-i version 3.4.2 (and the accompanying release notes). It is now ready for download. The release notes can be found here: https://open.med.harvard.edu/wiki/display/eaglei/3.4.2+Release+Notes+(Current+Release) This the latest and greatest version. Release notes for versions 3.2.0 & 3.3.0 can be found here: https://open.med.harvard.edu/wiki/display/eaglei/3.2.0+Release+Notes https://open.med.harvard.edu/wiki/display/eaglei/3.3.0+Release+Notes Some highlights of what you?ll find in these notes: * New search feature, using a federated SPARQL query for iPSC lines. * Move to requiring a public SPARQL endpoint * Location of navigation snippets have been changed * Embedded search bar updated for more styling flexibility Your patience is greatly appreciated. If you have any questions, comments or corrections regarding the documentation, please let us know. Kind Regards, 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 Fri Mar 27 13:12:34 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Fri, 27 Mar 2015 17:12:34 +0000 Subject: [Eagle-i-admins] eagle-i version 3.4.2 released & other release notes In-Reply-To: <6BEFC40F-4652-4D53-9015-AD9FC507840D@hms.harvard.edu> References: <6BEFC40F-4652-4D53-9015-AD9FC507840D@hms.harvard.edu> Message-ID: <2643CD07-343E-46B5-9F5B-D4A5E8D53411@dartmouth.edu> Hi Sophia, Is 3.4.2 now considered the stable release? I see 3.3.0 is still listed as the latest stable version and we're scheduled to do an update from 3.0.4. Best, --sukie-- > On Mar 26, 2015, at 6:27 PM, Cheng, Sophia wrote: > > Dear eagle-i Sys Admins, > > We are pleased to announce the release of eagle-i version 3.4.2 (and the accompanying release notes). It is now ready for download. > > The release notes can be found here: https://open.med.harvard.edu/wiki/display/eaglei/3.4.2+Release+Notes+(Current+Release) > > This the latest and greatest version. Release notes for versions 3.2.0 & 3.3.0 can be found here: > https://open.med.harvard.edu/wiki/display/eaglei/3.2.0+Release+Notes > https://open.med.harvard.edu/wiki/display/eaglei/3.3.0+Release+Notes > > Some highlights of what you?ll find in these notes: > ? New search feature, using a federated SPARQL query for iPSC lines. > ? Move to requiring a public SPARQL endpoint > ? Location of navigation snippets have been changed > ? Embedded search bar updated for more styling flexibility > > Your patience is greatly appreciated. If you have any questions, comments or corrections regarding the documentation, please let us know. > > Kind Regards, > 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 > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins From Michael_Cherry at hms.harvard.edu Fri Mar 27 13:38:24 2015 From: Michael_Cherry at hms.harvard.edu (Cherry, Michael) Date: Fri, 27 Mar 2015 13:38:24 -0400 Subject: [Eagle-i-admins] eagle-i version 3.4.2 released & other release notes In-Reply-To: <2643CD07-343E-46B5-9F5B-D4A5E8D53411@dartmouth.edu> References: <6BEFC40F-4652-4D53-9015-AD9FC507840D@hms.harvard.edu> <2643CD07-343E-46B5-9F5B-D4A5E8D53411@dartmouth.edu> Message-ID: <2D9A56628D03E943A293017B10EFD25C01013EE19BBA@ITCCRMAIL01.MED.HARVARD.EDU> > Is 3.4.2 now considered the stable release? I see 3.3.0 is still listed as > the latest stable version and we're scheduled to do an update from 3.0.4. Hi Sukie, I apologize! We neglected to update the downloads page after the release of 3.4.2. I'll update it right now. It will be corrected by 2:00 (Eastern) today. - Mike C From Sukdith.Punjasthitkul at dartmouth.edu Fri Mar 27 13:44:35 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Fri, 27 Mar 2015 17:44:35 +0000 Subject: [Eagle-i-admins] eagle-i version 3.4.2 released & other release notes In-Reply-To: <2D9A56628D03E943A293017B10EFD25C01013EE19BBA@ITCCRMAIL01.MED.HARVARD.EDU> References: <6BEFC40F-4652-4D53-9015-AD9FC507840D@hms.harvard.edu> <2643CD07-343E-46B5-9F5B-D4A5E8D53411@dartmouth.edu> <2D9A56628D03E943A293017B10EFD25C01013EE19BBA@ITCCRMAIL01.MED.HARVARD.EDU> Message-ID: <861B16E7-0A11-4CC5-9D3B-E5A111BC57EA@dartmouth.edu> No worries :) I'll download the 3.4.2 release now. Thanks! --sukie-- > On Mar 27, 2015, at 1:38 PM, Cherry, Michael wrote: > >> Is 3.4.2 now considered the stable release? I see 3.3.0 is still listed as >> the latest stable version and we're scheduled to do an update from 3.0.4. > > Hi Sukie, > > I apologize! We neglected to update the downloads page after the release of 3.4.2. > > I'll update it right now. It will be corrected by 2:00 (Eastern) today. > > - Mike C > From Sophia_Cheng at hms.harvard.edu Sat Mar 28 20:00:37 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Sat, 28 Mar 2015 20:00:37 -0400 Subject: [Eagle-i-admins] New documentation available Message-ID: <07769101-CF8E-4642-AC07-6A51E20C77E3@hms.harvard.edu> Dear wonderful sys admins, In response to questions we?ve received regarding how to upgrade from a much older version to a newer one, we have put together a data migration guide to assist you: https://open.med.harvard.edu/wiki/display/eaglei/Data+Migration+Guide. Additionally, release notes for versions 3.1.1 to 3.4.2 now reference an upgrade checklist to help with upgrading: https://open.med.harvard.edu/wiki/display/eaglei/Upgrade+Checklist. We hope these documents will help you with upgrading. Please let us know if you have any comments or questions. Thanks, 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 Tue Mar 31 10:34:57 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Tue, 31 Mar 2015 14:34:57 +0000 Subject: [Eagle-i-admins] [ eagle-i-admins ] Broken link in SWEET when upgrading to 3.4.2, public sparqler issues Message-ID: <2E9996F4-D9B1-4343-874F-9B7D6DB180D4@dartmouth.edu> 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 Tue Mar 31 12:09:26 2015 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Tue, 31 Mar 2015 12:09:26 -0400 Subject: [Eagle-i-admins] [ eagle-i-admins ] Broken link in SWEET when upgrading to 3.4.2, public sparqler issues In-Reply-To: <2E9996F4-D9B1-4343-874F-9B7D6DB180D4@dartmouth.edu> References: <2E9996F4-D9B1-4343-874F-9B7D6DB180D4@dartmouth.edu> Message-ID: 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: