<div dir="ltr">Hi Sophia,<div><br></div><div style>We restarted tomcat, and now the ontology browser link is functional.</div><div style><br></div><div style><span style="font-family:arial,sans-serif;font-size:13px">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".</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Directory structure of ~tomcat:</span><br style="font-family:arial,sans-serif;font-size:13px"><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">/usr/share/tomcat6/</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">├── bin</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">└── eaglei</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> └── sparqler</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> ├── logs</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> └── sesame</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Directory structure of /opt/tomcat/work:</span><br style="font-family:arial,sans-serif;font-size:13px"><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">/opt/tomcat/work/</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">└── Catalina</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> └── localhost</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> ├── _</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ └── org</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> │ └── apache</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ └── jsp</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> │ └── repository</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ ├── admin</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> │ ├── logout</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ └── query</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> ├── ${catalina.base}</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> ├── docs</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> ├── examples</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> ├── help</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> ├── host-manager</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> ├── institution</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> ├── manager</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ └── org</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> │ └── apache</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ └── jsp</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> │ └── WEB_002dINF</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ └── jsp</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> ├── ROOT.orig</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> ├── sparqler</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> │ └── org</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ └── apache</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> │ └── jsp</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ ├── query</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> │ └── repository</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> │ └── admin</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> └── sweet</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> └── org</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> └── apache</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> └── jsp</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> ├── cores</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> ├── feedback</span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px"> └── labs</span><br style="font-family:arial,sans-serif;font-size:13px">
<br style="font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px">Should we delete /opt/tomcat/work?</span><br style="font-family:arial,sans-serif;font-size:13px"></div><div style>
<span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div style><span style="font-family:arial,sans-serif;font-size:13px">Thanks,</span></div><div style><span style="font-family:arial,sans-serif;font-size:13px">Faith</span></div>
</div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><div>Faith Coldren, PhD</div><div>Biomedical Data Curator</div><div>ITMAT</div><div>University of Pennsylvania</div><div>215-573-9462</div><div>************************************</div>
<div>Discover.Accelerate.Promote</div><div><a href="https://eagle-i.itmat.upenn.edu" target="_blank">https://eagle-i.itmat.upenn.edu</a></div></div></div>
<br><br><div class="gmail_quote">On Wed, Feb 26, 2014 at 10:54 AM, Cheng, Sophia <span dir="ltr"><<a href="mailto:Sophia_Cheng@hms.harvard.edu" target="_blank">Sophia_Cheng@hms.harvard.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Faith,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Thanks for your patience. Please let us know if you continue to have trouble with the ontology browser link in the top navigation.<br>
<br>
Sincerely,<br>
Sophia<br>
<div class="HOEnZb"><div class="h5"><br>
On Jan 31, 2014, at 5:10 PM, "Cherry, Michael" <<a href="mailto:Michael_Cherry@hms.harvard.edu">Michael_Cherry@hms.harvard.edu</a>> wrote:<br>
<br>
>> I updated property value for eagle.model.url.<br>
>> This fixed the problem.<br>
><br>
>> Could you suggest where I should change the Ontology<br>
>> Browser link for the header in SWEET so that users<br>
>> have a functioning link?<br>
><br>
> Hi Faith,<br>
><br>
> I'm not sure but I don't know if the links in the application headers are locally configurable.<br>
><br>
> We'll get an answer to you within the next few days.<br>
><br>
> - Mike C<br>
><br>
><br>
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