[Eagle-i-admins] Auto-complete in SWEET not working and Ontology Browser down

[Cheng, Sophia]

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 <fcoldren at mail.med.upenn.edu<mailto:fcoldren at mail.med.upenn.edu>> 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<https://eagle-i.itmat.upenn.edu/>


On Wed, Feb 26, 2014 at 10:54 AM, Cheng, Sophia <Sophia_Cheng at hms.harvard.edu<mailto: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<mailto: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
>
>
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