It appears as though the UI cannot talk to the REST services based on the
`Errno::ECONNREFUSED:
Connection refused` error. (01)
Paul (02)
On Oct 26, 2013, at 6:38 AM, Peter Yim <peter.yim@xxxxxxxx> wrote: (03)
> Thank you, Shinya, Nancy & Gary.
>
>
> 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.)
>
>
> Thanks & regards. =ppy
> --
>
>
>
> On Friday, October 25, 2013 8:19 PM, YAMADA Shinya
> <shinya.yamada@xxxxxxxxx> wrote:
>
> Peter,
>
> 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.
>
>
> 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"}
>
> 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'
>
> Thanks,
>
> ___
> Shinya
>
>
>
> ---------- 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>
>
>
> Thank you, Nancy ... that's what I needed to find out.
>
> This will help a lot when we try to diagnose what caused the "error"
>condition.
>
> Regards. =ppy
> --
>
>
> 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
>
>
>
> 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.
>>>>
>>>>
>>
>> (04)
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