<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Hi Todd,</div><div><br></div><div>Regarding the configuration files, we are attempting to simplify examples and have moved them to this location:</div><div><br></div><div><a href="https://open.med.harvard.edu/svn/eagle-i-dev/apps/trunk/configuration/src/main/resources/examples/">https://open.med.harvard.edu/svn/eagle-i-dev/apps/trunk/configuration/src/main/resources/examples/</a></div><div><br></div><div>Where we have example configuration files for various set ups, instead of having one giant file with all the options listed.</div><div><br></div><div>As to where your institution home page went .. I'm not sure. That page is served from your repository, so you could check if this file exists:</div><div><br></div><div>/usr/share/tomcat7/webapps/ROOT/index.jsp</div><div><br></div><div>This is the file that produces that home page. If you see that page, I would check the repository log to see if there is some error occurring while trying to substitute values in. </div><div><br></div><div>One thing that comes to mind is that you said you created an external hostname. Did you update this in the repository's configuration? This may be the problem.</div><div><br></div><div>Let me know if that helps or not.</div><div><br></div><div>Sincerely,</div><div>Sophia</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Todd Hall <<a href="mailto:halltodd@msu.edu">halltodd@msu.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, November 26, 2013 5:28 PM<br><span style="font-weight:bold">To: </span> Sophia <<a href="mailto:sophia_cheng@hms.harvard.edu">sophia_cheng@hms.harvard.edu</a>><br><span style="font-weight:bold">Cc: </span> eagle-i-admins <<a href="mailto:eagle-i-admins@open.med.harvard.edu">eagle-i-admins@open.med.harvard.edu</a>>, Jonathan Babbage <<a href="mailto:Jonathan.Babbage@hc.msu.edu">Jonathan.Babbage@hc.msu.edu</a>><br><span style="font-weight:bold">Subject: </span> RE: Failed to load ontology question<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta name="Generator" content="Microsoft Word 14 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
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</o:shapelayout></xml><![endif]--><div lang="EN-US" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Hello Sophia,<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Thank you for responding. I’m running the Repository, Sweet and Institutional search applications. I figured out the login situation with the Sweet App.
I was using an internal only hostname.domain. I’ve since created an external hostname and can get in via Sweet. However, I’m having issues with the “Institution Home” link on the Sweet page. It points to the root, like it should, but I get an error about
redirecting: example: “Firefox has detected that the server is redirecting the request for this address in a way that will never complete”. The odd thing about the Institution Home link, is that before I loaded the sweet.war and help.war files into tomcat,
that link worked as it does on your training site, training.eagle-i.net:8443<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">I noticed that the example configuration file links are broken:
<a href="https://open.med.harvard.edu/svn/eagle-i-dev/apps/trunk/examples/config-files">
https://open.med.harvard.edu/svn/eagle-i-dev/apps/trunk/examples/config-files</a><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">If you like to see what I’ve done, here are the two accessible links:
<a href="http://eagle-i.ctsi.msu.edu/sweet">http://eagle-i.ctsi.msu.edu/sweet</a> and
<a href="http://eagle-i.ctsi.msu.edu/institution">http://eagle-i.ctsi.msu.edu/institution</a><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">The footer for both sites:
<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Copyright © 2013 by the President and Fellows of Harvard College<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Application Version: 2.0-MS2.20 15870 2013-10-28 15:48:10<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">/
<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Ontology Version: 1.8.3.1 15260 2013-07-02 14:38:44<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Best Regards,<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Todd E. Hall
<img border="0" width="23" height="26" id="Picture_x0020_1" src="cid:image001.png@01CEEACC.68BE8F30" alt="spartan"><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Systems Administrator<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">-----------------------------------------------------<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Biomedical Research Informatics Core (BRIC)<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Clinical and Translational Sciences Institute (CTSI)<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Michigan State University - West Fee Hall<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">909 Fee Road, Room B510 – W1<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">East Lansing, Michigan 48824-1317<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Phone: (517) 884-2906<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">BRIC Helpline<b>:</b> (517) 643-2075</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p></o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><o:p> </o:p></span></p><div><div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in"><p class="MsoNormal"><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "> Cheng, Sophia [<a href="mailto:Sophia_Cheng@hms.harvard.edu">mailto:Sophia_Cheng@hms.harvard.edu</a>]
<br><b>Sent:</b> Tuesday, November 26, 2013 4:59 PM<br><b>To:</b> <a href="mailto:halltodd@msu.edu">halltodd@msu.edu</a><br><b>Cc:</b> eagle-i-admins<br><b>Subject:</b> Failed to load ontology question<o:p></o:p></span></p></div></div><p class="MsoNormal"><o:p> </o:p></p><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">Dear Todd,<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; "><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">I am copying our sys-admin mailing list in this response so that others might benefit from your question or might have run into a similar scenario. The initial
question is:<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; "><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">~~~<o:p></o:p></span></p></div><div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">I'm having trouble setting up the Eagle-i application. I can get the repository app installed; add users but when I click on "Show Data Model Ontology Model"
via the admin page, I get:<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">More Detail<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">loaded<span class="apple-tab-span">
</span>availableJar<span class="apple-tab-span"> </span>availableModel<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">"1.8.3.1 15260 2013-07-02 14:38:44"<span class="apple-tab-span">
</span>"1.8.3.1"<span class="apple-tab-span"> </span>"(failed or not in ontology)"<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">It's stating that its loaded and the version of the jar file but it failed. The installation never gave an error. It's a Centos 6.4 OS, VM running Tomcat 7.0.47
and Jdk1.7.0_45.<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">I'm almost certain this is the reason that I can't login via Sweet. It comes back to tell me that the repository isn't available.<o:p></o:p></span></p></div></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">~~~<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; "><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">To address your question, I need some more information:<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">-> Which applications are you running? SWEET? Institution Search? Repository?<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">+--> If you are running also Institution Search, does that come up? If yes, what is the information in the footer?<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">-> Are there any errors reported in the logs? The logs for the repository live separately than tomcat/logs. You can find the logs for the repository in the same
directory as your repository home directory, i.e. ../eaglei/repo/logs<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; "><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">Also, you can subscribe to the list here:
<a href="https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins">https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins</a>.<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; "><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">Thanks!<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; "><o:p> </o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">Sincerely,<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">Sophia<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; "><o:p> </o:p></span></p></div><div><div><div><p class="MsoNormal"><span style="font-size: 10.5pt; font-family: Calibri, sans-serif; color: black; ">-- <o:p></o:p></span></p></div><div><div><p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas;color:black">Sophia K. Cheng<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas;color:black">Software Technical Lead<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas;color:black">eagle-i @ Harvard University<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas;color:black">Vanderbilt Hall, 019<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas;color:black">107 Avenue Louis Pasteur<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas;color:black">Boston MA 02115<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas;color:black">Skype: sophia.k.cheng<o:p></o:p></span></p></div><div><p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas;color:black">Web: <a href="http://www.eagle-i.net/">www.eagle-i.net</a><o:p></o:p></span></p></div></div></div></div></div></div></div></span></body></html>