Thank you, Paul. (01)
Since the SOCoP-OOR instance (at: http://socop.oor.net/ontologies )
and the OOR-sandbox (at: http://sandbox.oor.net/ ) instance are not
appreciably different (and are only cosmetically different from the
ncbo-appliance vm code-wise) ... could you suggest some plausible
cause why the former is returning the error, while the latter seems to
be functioning ok? [attn: Paul & Ken] (02)
Thanks & regards. =ppy
-- (03)
On Mon, Oct 28, 2013 at 10:21 AM, Paul R Alexander
<palexander@xxxxxxxxxxxx> wrote:
> It appears as though the UI cannot talk to the REST services based on the
>`Errno::ECONNREFUSED:
> Connection refused` error.
>
> Paul
>
>
> On Oct 26, 2013, at 6:38 AM, Peter Yim <peter.yim@xxxxxxxx> wrote:
>
>> 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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