From Sophia_Cheng at hms.harvard.edu Wed Feb 26 10:54:35 2014 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Wed, 26 Feb 2014 10:54:35 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: <2D9A56628D03E943A293017B10EFD25CD6362E9AAE@ITCCRMAIL01.MED.HARVARD.EDU> References: <294F7BCA-02C2-48F9-8DF1-CC3C5DCC223D@hms.harvard.edu> <373358968.8630421.1391183473051.JavaMail.root@zimbra.upenn.edu> <2D9A56628D03E943A293017B10EFD25CD6362E9AAE@ITCCRMAIL01.MED.HARVARD.EDU> Message-ID: Hi Faith, The issue you were seeing with the ontology browser was due to a misconfiguration on our part (the navigation is pulling in the navigation from our server). We have fixed this and pushed the fix to the production tier. You will need to restart to pick up this change. When you restart, be sure to delete this folder ~tomcat/work. This is tomcat's working folder and we noticed that it was caching the link for the navigation. Thanks for your patience. Please let us know if you continue to have trouble with the ontology browser link in the top navigation. Sincerely, Sophia On Jan 31, 2014, at 5:10 PM, "Cherry, Michael" wrote: >> I updated property value for eagle.model.url. >> This fixed the problem. > >> Could you suggest where I should change the Ontology >> Browser link for the header in SWEET so that users >> have a functioning link? > > Hi Faith, > > I'm not sure but I don't know if the links in the application headers are locally configurable. > > We'll get an answer to you within the next few days. > > - Mike C > > > _______________________________________________ > 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 Wed Feb 26 14:27:15 2014 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Wed, 26 Feb 2014 14:27:15 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: References: <294F7BCA-02C2-48F9-8DF1-CC3C5DCC223D@hms.harvard.edu> <373358968.8630421.1391183473051.JavaMail.root@zimbra.upenn.edu> <2D9A56628D03E943A293017B10EFD25CD6362E9AAE@ITCCRMAIL01.MED.HARVARD.EDU> Message-ID: Hi Sophia, We restarted tomcat, and now the ontology browser link is functional. However, we don't see a directory called "work" under ~tomcat. There is a "work" directory under /opt/tomcat/ and inside this directory is another directory called "Catalina". Directory structure of ~tomcat: /usr/share/tomcat6/ ??? bin ??? eaglei ??? sparqler ??? logs ??? sesame Directory structure of /opt/tomcat/work: /opt/tomcat/work/ ??? Catalina ??? localhost ??? _ ? ??? org ? ??? apache ? ??? jsp ? ??? repository ? ??? admin ? ??? logout ? ??? query ??? ${catalina.base} ??? docs ??? examples ??? help ??? host-manager ??? institution ??? manager ? ??? org ? ??? apache ? ??? jsp ? ??? WEB_002dINF ? ??? jsp ??? ROOT.orig ??? sparqler ? ??? org ? ??? apache ? ??? jsp ? ??? query ? ??? repository ? ??? admin ??? sweet ??? org ??? apache ??? jsp ??? cores ??? feedback ??? labs Should we delete /opt/tomcat/work? Thanks, Faith Faith Coldren, PhD Biomedical Data Curator ITMAT University of Pennsylvania 215-573-9462 ************************************ Discover.Accelerate.Promote https://eagle-i.itmat.upenn.edu On Wed, Feb 26, 2014 at 10:54 AM, Cheng, Sophia < Sophia_Cheng at hms.harvard.edu> wrote: > Hi Faith, > > The issue you were seeing with the ontology browser was due to a > misconfiguration on our part (the navigation is pulling in the navigation > from our server). We have fixed this and pushed the fix to the production > tier. > > You will need to restart to pick up this change. When you restart, be > sure to delete this folder ~tomcat/work. This is tomcat's working folder > and we noticed that it was caching the link for the navigation. > > Thanks for your patience. Please let us know if you continue to have > trouble with the ontology browser link in the top navigation. > > Sincerely, > Sophia > > On Jan 31, 2014, at 5:10 PM, "Cherry, Michael" < > Michael_Cherry at hms.harvard.edu> wrote: > > >> I updated property value for eagle.model.url. > >> This fixed the problem. > > > >> Could you suggest where I should change the Ontology > >> Browser link for the header in SWEET so that users > >> have a functioning link? > > > > Hi Faith, > > > > I'm not sure but I don't know if the links in the application headers > are locally configurable. > > > > We'll get an answer to you within the next few days. > > > > - Mike C > > > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://open.med.harvard.edu/pipermail/eagle-i-admins/attachments/20140226/dbd8afe8/attachment.html From Sophia_Cheng at hms.harvard.edu Wed Feb 26 14:30:30 2014 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Wed, 26 Feb 2014 14:30:30 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: References: <294F7BCA-02C2-48F9-8DF1-CC3C5DCC223D@hms.harvard.edu> <373358968.8630421.1391183473051.JavaMail.root@zimbra.upenn.edu> <2D9A56628D03E943A293017B10EFD25CD6362E9AAE@ITCCRMAIL01.MED.HARVARD.EDU> Message-ID: <7DE20A90-135F-4EA1-B80D-758A0F73F6C1@hms.harvard.edu> Hi Faith, If your ontology browser is working, then there's no need to worry about the "work" directory. That might have just been a weird edge case in our servers. Sincerely, Sophia On Feb 26, 2014, at 2:27 PM, Faith Coldren > wrote: Hi Sophia, We restarted tomcat, and now the ontology browser link is functional. However, we don't see a directory called "work" under ~tomcat. There is a "work" directory under /opt/tomcat/ and inside this directory is another directory called "Catalina". Directory structure of ~tomcat: /usr/share/tomcat6/ ??? bin ??? eaglei ??? sparqler ??? logs ??? sesame Directory structure of /opt/tomcat/work: /opt/tomcat/work/ ??? Catalina ??? localhost ??? _ ? ??? org ? ??? apache ? ??? jsp ? ??? repository ? ??? admin ? ??? logout ? ??? query ??? ${catalina.base} ??? docs ??? examples ??? help ??? host-manager ??? institution ??? manager ? ??? org ? ??? apache ? ??? jsp ? ??? WEB_002dINF ? ??? jsp ??? ROOT.orig ??? sparqler ? ??? org ? ??? apache ? ??? jsp ? ??? query ? ??? repository ? ??? admin ??? sweet ??? org ??? apache ??? jsp ??? cores ??? feedback ??? labs Should we delete /opt/tomcat/work? Thanks, Faith Faith Coldren, PhD Biomedical Data Curator ITMAT University of Pennsylvania 215-573-9462 ************************************ Discover.Accelerate.Promote https://eagle-i.itmat.upenn.edu On Wed, Feb 26, 2014 at 10:54 AM, Cheng, Sophia > wrote: Hi Faith, The issue you were seeing with the ontology browser was due to a misconfiguration on our part (the navigation is pulling in the navigation from our server). We have fixed this and pushed the fix to the production tier. You will need to restart to pick up this change. When you restart, be sure to delete this folder ~tomcat/work. This is tomcat's working folder and we noticed that it was caching the link for the navigation. Thanks for your patience. Please let us know if you continue to have trouble with the ontology browser link in the top navigation. Sincerely, Sophia On Jan 31, 2014, at 5:10 PM, "Cherry, Michael" > wrote: >> I updated property value for eagle.model.url. >> This fixed the problem. > >> Could you suggest where I should change the Ontology >> Browser link for the header in SWEET so that users >> have a functioning link? > > Hi Faith, > > I'm not sure but I don't know if the links in the application headers are locally configurable. > > We'll get an answer to you within the next few days. > > - Mike C > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: https://open.med.harvard.edu/pipermail/eagle-i-admins/attachments/20140226/b4244ad7/attachment-0001.html From fcoldren at mail.med.upenn.edu Wed Feb 26 14:40:06 2014 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Wed, 26 Feb 2014 14:40:06 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: <7DE20A90-135F-4EA1-B80D-758A0F73F6C1@hms.harvard.edu> References: <294F7BCA-02C2-48F9-8DF1-CC3C5DCC223D@hms.harvard.edu> <373358968.8630421.1391183473051.JavaMail.root@zimbra.upenn.edu> <2D9A56628D03E943A293017B10EFD25CD6362E9AAE@ITCCRMAIL01.MED.HARVARD.EDU> <7DE20A90-135F-4EA1-B80D-758A0F73F6C1@hms.harvard.edu> Message-ID: Understood. Thank you! Faith Coldren, PhD Biomedical Data Curator ITMAT University of Pennsylvania 215-573-9462 ************************************ Discover.Accelerate.Promote https://eagle-i.itmat.upenn.edu On Wed, Feb 26, 2014 at 2:30 PM, Cheng, Sophia wrote: > Hi Faith, > > If your ontology browser is working, then there's no need to worry about > the "work" directory. That might have just been a weird edge case in our > servers. > > Sincerely, > Sophia > > > On Feb 26, 2014, at 2:27 PM, Faith Coldren > wrote: > > Hi Sophia, > > We restarted tomcat, and now the ontology browser link is functional. > > However, we don't see a directory called "work" under ~tomcat. There is a > "work" directory under /opt/tomcat/ and inside this directory is another > directory called "Catalina". > > Directory structure of ~tomcat: > > /usr/share/tomcat6/ > ??? bin > ??? eaglei > ??? sparqler > ??? logs > ??? sesame > > Directory structure of /opt/tomcat/work: > > /opt/tomcat/work/ > ??? Catalina > ??? localhost > ??? _ > ? ??? org > ? ??? apache > ? ??? jsp > ? ??? repository > ? ??? admin > ? ??? logout > ? ??? query > ??? ${catalina.base} > ??? docs > ??? examples > ??? help > ??? host-manager > ??? institution > ??? manager > ? ??? org > ? ??? apache > ? ??? jsp > ? ??? WEB_002dINF > ? ??? jsp > ??? ROOT.orig > ??? sparqler > ? ??? org > ? ??? apache > ? ??? jsp > ? ??? query > ? ??? repository > ? ??? admin > ??? sweet > ??? org > ??? apache > ??? jsp > ??? cores > ??? feedback > ??? labs > > Should we delete /opt/tomcat/work? > > Thanks, > Faith > > Faith Coldren, PhD > Biomedical Data Curator > ITMAT > University of Pennsylvania > 215-573-9462 > ************************************ > Discover.Accelerate.Promote > https://eagle-i.itmat.upenn.edu > > > On Wed, Feb 26, 2014 at 10:54 AM, Cheng, Sophia < > Sophia_Cheng at hms.harvard.edu> wrote: > >> Hi Faith, >> >> The issue you were seeing with the ontology browser was due to a >> misconfiguration on our part (the navigation is pulling in the navigation >> from our server). We have fixed this and pushed the fix to the production >> tier. >> >> You will need to restart to pick up this change. When you restart, be >> sure to delete this folder ~tomcat/work. This is tomcat's working folder >> and we noticed that it was caching the link for the navigation. >> >> Thanks for your patience. Please let us know if you continue to have >> trouble with the ontology browser link in the top navigation. >> >> Sincerely, >> Sophia >> >> On Jan 31, 2014, at 5:10 PM, "Cherry, Michael" < >> Michael_Cherry at hms.harvard.edu> wrote: >> >> >> I updated property value for eagle.model.url. >> >> This fixed the problem. >> > >> >> Could you suggest where I should change the Ontology >> >> Browser link for the header in SWEET so that users >> >> have a functioning link? >> > >> > Hi Faith, >> > >> > I'm not sure but I don't know if the links in the application headers >> are locally configurable. >> > >> > We'll get an answer to you within the next few days. >> > >> > - Mike C >> > >> > >> > _______________________________________________ >> > 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 >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://open.med.harvard.edu/pipermail/eagle-i-admins/attachments/20140226/da6d5f9c/attachment.html From Michael_Cherry at hms.harvard.edu Wed Feb 26 16:34:52 2014 From: Michael_Cherry at hms.harvard.edu (Cherry, Michael) Date: Wed, 26 Feb 2014 16:34:52 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: References: <294F7BCA-02C2-48F9-8DF1-CC3C5DCC223D@hms.harvard.edu> <373358968.8630421.1391183473051.JavaMail.root@zimbra.upenn.edu> <2D9A56628D03E943A293017B10EFD25CD6362E9AAE@ITCCRMAIL01.MED.HARVARD.EDU> <7DE20A90-135F-4EA1-B80D-758A0F73F6C1@hms.harvard.edu> Message-ID: <2D9A56628D03E943A293017B10EFD25CFEC691710E@ITCCRMAIL01.MED.HARVARD.EDU> > There is a "work" directory under /opt/tomcat/ and inside > this directory is another directory called "Catalina"... > Should we delete /opt/tomcat/work? Hi Faith, To be safe, you should delete that "work" directory every time you install a new version of the application. More often wouldn't hurt, but that's the minimum. regards, - Mike Cherry Sr. Release Operations Engineer Harvard Catalyst | Center for Biomedical Informatics Harvard Medical School