From fcoldren at mail.med.upenn.edu Thu Jan 30 16:27:04 2014 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Thu, 30 Jan 2014 16:27:04 -0500 (EST) Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: <2144649117.8368971.1391116739177.JavaMail.root@zimbra.upenn.edu> Message-ID: <1064957447.8372703.1391117224655.JavaMail.root@zimbra.upenn.edu> Hi, Just now during data entry in SWEET, the auto-complete for fields populated with ontology terms stopped working. For example, when creating a new Organism or Virus record, the field "Organism or Virus Type" does not display options when I start typing "mus musc". We were able to replicate the issue in three different browsers (Chrome, Firefox and Safari) and for different resource types. I suggested that our curator use the Ontology Browser to figure out how to navigate to mus musculus through the drop-down box, but the Ontology Browser is down. We restarted the eagle-i applications on our server, but this did not fix the issue in SWEET. Is SWEET connected to the Ontology Browser? Is there anything we should do locally to fix the issue in SWEET? Thanks, Faith From Michael_Cherry at hms.harvard.edu Thu Jan 30 16:32:57 2014 From: Michael_Cherry at hms.harvard.edu (Cherry, Michael) Date: Thu, 30 Jan 2014 16:32:57 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: <1064957447.8372703.1391117224655.JavaMail.root@zimbra.upenn.edu> References: <2144649117.8368971.1391116739177.JavaMail.root@zimbra.upenn.edu> <1064957447.8372703.1391117224655.JavaMail.root@zimbra.upenn.edu> Message-ID: <2D9A56628D03E943A293017B10EFD25CD6362E99E5@ITCCRMAIL01.MED.HARVARD.EDU> Hi Faith, ... but the Ontology Browser is down. Leaving aside your other questions for the moment, by "ontology browser" do you mean https://search.eagle-i.net/model ? It's up and responsive for me right now. (I also haven't received any alerts today about any issues the underlying server, though of course that in and of itself is inconclusive) regards, - Mike Cherry Sr. Release Operations Engineer Harvard Catalyst | Center for Biomedical Informatics Harvard Medical School From Sophia_Cheng at hms.harvard.edu Thu Jan 30 16:56:22 2014 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Thu, 30 Jan 2014 16:56:22 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: <2D9A56628D03E943A293017B10EFD25CD6362E99E5@ITCCRMAIL01.MED.HARVARD.EDU> References: <2144649117.8368971.1391116739177.JavaMail.root@zimbra.upenn.edu> <1064957447.8372703.1391117224655.JavaMail.root@zimbra.upenn.edu> <2D9A56628D03E943A293017B10EFD25CD6362E99E5@ITCCRMAIL01.MED.HARVARD.EDU> Message-ID: Hi Faith, Thank you for your thorough investigation into the issue. We recently made a change to our servers which has caused some of the links in the header and footer of the application to fail. If you or your curator arrived at the Ontology Browser via one of these links, it is expected that it will fail. We are fixing this issue and it will be reflected tomorrow. In the meantime, you can access the Browser by navigating to https://search.eagle-i.net/model directly. We're looking into what might be happening with your SWEET. This issue is not showing up in the 2 other nodes we've looked at. Could you try going straight to the Ontology Browser with the above link and let me know if you are able to view & use it? Sincerely, Sophia ---- Sophia K. Cheng Software Technical Lead eagle-i @ Harvard University Vanderbilt Hall, 019 107 Avenue Louis Pasteur Boston MA 02115 Skype: sophia.k.cheng Web: www.eagle-i.net On Jan 30, 2014, at 4:32 PM, "Cherry, Michael" > wrote: Hi Faith, ... but the Ontology Browser is down. Leaving aside your other questions for the moment, by "ontology browser" do you mean https://search.eagle-i.net/model ? It's up and responsive for me right now. (I also haven't received any alerts today about any issues the underlying server, though of course that in and of itself is inconclusive) regards, - Mike Cherry Sr. Release Operations Engineer Harvard Catalyst | Center for Biomedical Informatics Harvard Medical School _______________________________________________ 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/20140130/d64ecef1/attachment.html From fcoldren at mail.med.upenn.edu Thu Jan 30 17:10:18 2014 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Thu, 30 Jan 2014 17:10:18 -0500 (EST) Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: Message-ID: <506872637.8393743.1391119818826.JavaMail.root@zimbra.upenn.edu> Hi, I accessed the ontology browser through the header of SWEET: https://search.eagle-i.net:8443/model/ I was able to access https://search.eagle-i.net/model and use the ontology browser. Thank you for investigating the problem. Faith ----- Original Message ----- From: "Sophia Cheng" To: "Michael Cherry" Cc: "Faith Coldren" , eagle-i-admins at open.med.harvard.edu Sent: Thursday, January 30, 2014 4:56:22 PM Subject: Re: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down Hi Faith, Thank you for your thorough investigation into the issue. We recently made a change to our servers which has caused some of the links in the header and footer of the application to fail. If you or your curator arrived at the Ontology Browser via one of these links, it is expected that it will fail. We are fixing this issue and it will be reflected tomorrow. In the meantime, you can access the Browser by navigating to https://search.eagle-i.net/model directly. We're looking into what might be happening with your SWEET. This issue is not showing up in the 2 other nodes we've looked at. Could you try going straight to the Ontology Browser with the above link and let me know if you are able to view & use it? Sincerely, Sophia ---- Sophia K. Cheng Software Technical Lead eagle-i @ Harvard University Vanderbilt Hall, 019 107 Avenue Louis Pasteur Boston MA 02115 Skype: sophia.k.cheng Web: www.eagle-i.net On Jan 30, 2014, at 4:32 PM, "Cherry, Michael" < Michael_Cherry at hms.harvard.edu > wrote: Hi Faith, ... but the Ontology Browser is down. Leaving aside your other questions for the moment, by "ontology browser" do you mean https://search.eagle-i.net/model ? It's up and responsive for me right now. (I also haven't received any alerts today about any issues the underlying server, though of course that in and of itself is inconclusive) regards, - Mike Cherry Sr. Release Operations Engineer Harvard Catalyst | Center for Biomedical Informatics Harvard Medical School _______________________________________________ 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 Jan 30 17:28:53 2014 From: Sophia_Cheng at hms.harvard.edu (Cheng, Sophia) Date: Thu, 30 Jan 2014 17:28:53 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: <506872637.8393743.1391119818826.JavaMail.root@zimbra.upenn.edu> References: <506872637.8393743.1391119818826.JavaMail.root@zimbra.upenn.edu> Message-ID: <294F7BCA-02C2-48F9-8DF1-CC3C5DCC223D@hms.harvard.edu> Hi Faith, Regarding your issues with the autosuggest in SWEET: I believe there may be a misconfigured property in the eagle-i-apps.properties file. Could you check that the following property is set to the given value: eaglei.model.url = https://search.eagle-i.net/model This property tells SWEET where to go to get term suggestions. -Sophia ---- Sophia K. Cheng Software Technical Lead eagle-i @ Harvard University Vanderbilt Hall, 019 107 Avenue Louis Pasteur Boston MA 02115 Skype: sophia.k.cheng Web: www.eagle-i.net On Jan 30, 2014, at 5:10 PM, Faith Coldren wrote: > Hi, > > I accessed the ontology browser through the header of SWEET: https://search.eagle-i.net:8443/model/ > > I was able to access https://search.eagle-i.net/model and use the ontology browser. > > Thank you for investigating the problem. > > Faith > > ----- Original Message ----- > From: "Sophia Cheng" > To: "Michael Cherry" > Cc: "Faith Coldren" , eagle-i-admins at open.med.harvard.edu > Sent: Thursday, January 30, 2014 4:56:22 PM > Subject: Re: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down > > Hi Faith, > > > Thank you for your thorough investigation into the issue. > > > We recently made a change to our servers which has caused some of the links in the header and footer of the application to fail. If you or your curator arrived at the Ontology Browser via one of these links, it is expected that it will fail. We are fixing this issue and it will be reflected tomorrow. In the meantime, you can access the Browser by navigating to https://search.eagle-i.net/model directly. > > > We're looking into what might be happening with your SWEET. This issue is not showing up in the 2 other nodes we've looked at. > > > Could you try going straight to the Ontology Browser with the above link and let me know if you are able to view & use it? > > > Sincerely, > Sophia > > > > ---- > Sophia K. Cheng > Software Technical Lead > eagle-i @ Harvard University > Vanderbilt Hall, 019 > 107 Avenue Louis Pasteur > Boston MA 02115 > Skype: sophia.k.cheng > Web: www.eagle-i.net > > > > > > On Jan 30, 2014, at 4:32 PM, "Cherry, Michael" < Michael_Cherry at hms.harvard.edu > wrote: > > > Hi Faith, > > ... but the Ontology Browser is down. > > Leaving aside your other questions for the moment, by "ontology browser" do you mean https://search.eagle-i.net/model ? > > It's up and responsive for me right now. (I also haven't received any alerts today about any issues the underlying server, though of course that in and of itself is inconclusive) > > regards, > - Mike Cherry > Sr. Release Operations Engineer > Harvard Catalyst | Center for Biomedical Informatics > Harvard Medical School > > > _______________________________________________ > 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 Fri Jan 31 10:51:13 2014 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Fri, 31 Jan 2014 10:51:13 -0500 (EST) Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: <294F7BCA-02C2-48F9-8DF1-CC3C5DCC223D@hms.harvard.edu> Message-ID: <373358968.8630421.1391183473051.JavaMail.root@zimbra.upenn.edu> Hi, 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? Thanks for your help! Faith ----- Original Message ----- From: "Sophia Cheng" To: "Faith Coldren" Cc: eagle-i-admins at open.med.harvard.edu, "Michael Cherry" Sent: Thursday, January 30, 2014 5:28:53 PM Subject: Re: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down Hi Faith, Regarding your issues with the autosuggest in SWEET: I believe there may be a misconfigured property in the eagle-i-apps.properties file. Could you check that the following property is set to the given value: eaglei.model.url = https://search.eagle-i.net/model This property tells SWEET where to go to get term suggestions. -Sophia ---- Sophia K. Cheng Software Technical Lead eagle-i @ Harvard University Vanderbilt Hall, 019 107 Avenue Louis Pasteur Boston MA 02115 Skype: sophia.k.cheng Web: www.eagle-i.net On Jan 30, 2014, at 5:10 PM, Faith Coldren wrote: > Hi, > > I accessed the ontology browser through the header of SWEET: https://search.eagle-i.net:8443/model/ > > I was able to access https://search.eagle-i.net/model and use the ontology browser. > > Thank you for investigating the problem. > > Faith > > ----- Original Message ----- > From: "Sophia Cheng" > To: "Michael Cherry" > Cc: "Faith Coldren" , eagle-i-admins at open.med.harvard.edu > Sent: Thursday, January 30, 2014 4:56:22 PM > Subject: Re: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down > > Hi Faith, > > > Thank you for your thorough investigation into the issue. > > > We recently made a change to our servers which has caused some of the links in the header and footer of the application to fail. If you or your curator arrived at the Ontology Browser via one of these links, it is expected that it will fail. We are fixing this issue and it will be reflected tomorrow. In the meantime, you can access the Browser by navigating to https://search.eagle-i.net/model directly. > > > We're looking into what might be happening with your SWEET. This issue is not showing up in the 2 other nodes we've looked at. > > > Could you try going straight to the Ontology Browser with the above link and let me know if you are able to view & use it? > > > Sincerely, > Sophia > > > > ---- > Sophia K. Cheng > Software Technical Lead > eagle-i @ Harvard University > Vanderbilt Hall, 019 > 107 Avenue Louis Pasteur > Boston MA 02115 > Skype: sophia.k.cheng > Web: www.eagle-i.net > > > > > > On Jan 30, 2014, at 4:32 PM, "Cherry, Michael" < Michael_Cherry at hms.harvard.edu > wrote: > > > Hi Faith, > > ... but the Ontology Browser is down. > > Leaving aside your other questions for the moment, by "ontology browser" do you mean https://search.eagle-i.net/model ? > > It's up and responsive for me right now. (I also haven't received any alerts today about any issues the underlying server, though of course that in and of itself is inconclusive) > > regards, > - Mike Cherry > Sr. Release Operations Engineer > Harvard Catalyst | Center for Biomedical Informatics > Harvard Medical School > > > _______________________________________________ > 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 Jan 31 17:10:23 2014 From: Michael_Cherry at hms.harvard.edu (Cherry, Michael) Date: Fri, 31 Jan 2014 17:10:23 -0500 Subject: [Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down In-Reply-To: <373358968.8630421.1391183473051.JavaMail.root@zimbra.upenn.edu> References: <294F7BCA-02C2-48F9-8DF1-CC3C5DCC223D@hms.harvard.edu> <373358968.8630421.1391183473051.JavaMail.root@zimbra.upenn.edu> Message-ID: <2D9A56628D03E943A293017B10EFD25CD6362E9AAE@ITCCRMAIL01.MED.HARVARD.EDU> > 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