Thank you, Shinya, Nancy & Gary. (01)
Does anyone on this list - folks from the BioPortal development team,
in particular - has a clue on how we can get out of this?
(... Note that we are still running an old version of the ncbo-appliance vm.) (02)
Thanks & regards. =ppy
-- (03)
On Friday, October 25, 2013 8:19 PM, YAMADA Shinya
<shinya.yamada@xxxxxxxxx> wrote: (04)
Peter, (05)
You need to ask someone who know BioPortal. I saw errors like
following in the log file(/var/log/rails/BioPortal/production.log).
BioPortal failed to connect to some service
but I don't know what it is. (06)
processing OntologiesController#show (for 5.10.83.81 at 2013-10-25
20:16:43) [GET]
Parameters: {"id"=>"10041", "p"=>"terms", "conceptid"=>"resource:SIO_000000"} (07)
NoMethodError (undefined method `io' for #<Errno::ECONNREFUSED:
Connection refused - connect(2)>):
lib/BioPortalRestfulCore.rb:1167:in `get_xml'
lib/BioPortalRestfulCore.rb:564:in `getOntology'
app/models/data_access.rb:564:in `send'
app/models/data_access.rb:564:in `cache_pull'
app/models/data_access.rb:186:in `getOntology'
app/controllers/ontologies_controller.rb:178:in `terms'
app/controllers/ontologies_controller.rb:35:in `show' (08)
Thanks, (09)
___
Shinya (010)
---------- original message ----------
From: Peter Yim <peter.yim@xxxxxxxx>
Date: Fri, Oct 25, 2013 at 5:28 PM
Subject: Re: socop.oor.net
To: Nancy Wiegand <wiegand@xxxxxxxxxxx>
Cc: Gary Berg-Cross <gbergcross@xxxxxxxxx> (011)
Thank you, Nancy ... that's what I needed to find out. (012)
This will help a lot when we try to diagnose what caused the "error" condition. (013)
Regards. =ppy
-- (014)
On Fri, Oct 25, 2013 at 4:54 PM, Nancy Wiegand <wiegand@xxxxxxxxxxx> wrote:
> Peter/Gary-
> All I did was type socop.oor.net. I get:
> 'We're sorry but something has gone wrong. We have been notified of this
> error.'
> Am I accessing it incorrectly? I used a new Web browser and hit refresh.
>
> Nancy (015)
On Fri, Oct 25, 2013 at 3:41 PM, Gary Berg-Cross <gbergcross@xxxxxxxxx> wrote:
> Peter,
> I get this message when I land on the page.
>
> e're sorry but something has gone wrong. We have been notified of this
> error.
>
>
> Perhaps Nancy did not when she first tried....
>
> Gary Berg-Cross, Ph.D.
> gbergcross@xxxxxxxxx
> http://ontolog.cim3.net/cgi-bin/wiki.pl?GaryBergCross
> NSF INTEROP Project
> http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0955816
> SOCoP Executive Secretary
> Knowledge Strategies
> Potomac, MD
> 240-426-0770
>
>
> On Fri, Oct 25, 2013 at 6:38 PM, Peter Yim <peter.yim@xxxxxxxx> wrote:
>>
>> Thank you for the message, Nancy ...
>>
>> I assume when you first land on the site, the error wasn't there, was
>> it? (because that was how I left it when I write my email to you. ...
>> I actually even browsed the listing of the ontologies in the
>> repository, did a search, and went into one of two ontology's page,
>> too.)
>>
>> If that "error condition" (like what is showing now) wasn't the way
>> you found the site, can you tell what happened in between, please?
>>
>> ... glad you can move forward with your presentation without the
>> SOCoP-OOR fully functional again.
>>
>> Regards. =ppy
>> --
>>
>>
>>
>> On Fri, Oct 25, 2013 at 3:18 PM, Nancy Wiegand <wiegand@xxxxxxxxxxx>
>> wrote:
>> > I just tried it, and it's the same error. It doesn't have to be fixed
>> > for
>> > me. I have prior screen shots I can use for a talk.
>> > Nancy
>> >
>> >
>> > On 10/25/2013 5:16 AM, Peter Yim wrote:
>> >
>> > Thanks to support from Shinya ...
>> >
>> > The SOCoP-OOR is restored now. It dis looklike everything is working ...
>> > but
>> > please double check to make sure.
>> >
>> > Thanks & regards. =ppy
>> >
>> > p.s. noting that it was an oor/bioportal software error that did not
>> > seem to
>> > be recoverable ... and the vm was actually still running (before we had
>> > to
>> > shut it down.)
>> > --
>> >
>> > On Oct 22, 2013 2:18 PM, "Peter Yim" <peter.yim@xxxxxxxx> wrote:
>> >>
>> >> Thank you for the notification ... Let us look into it. I'll let you
>> >> know
>> >> if I have further news.
>> >>
>> >> Regards. =ppy
>> >> --
>> >>
>> >> On Oct 22, 2013 1:48 PM, "Nancy Wiegand" <wiegand@xxxxxxxxxxx> wrote:
>> >>>
>> >>> is down.
>> >
>> >
>
> (016)
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