If they are pointed at different REST back-ends (or hosted as two separate
self-contained VMs) then one back-end service may be up while the other is
down. If they are pointing to the same back-end REST instance and the UI is not
on the same machine, there could be connectivity problems between the UI
machine and the REST machine. (01)
Paul (02)
On Oct 28, 2013, at 10:33 AM, Peter Yim <peter.yim@xxxxxxxx> wrote: (03)
> Thank you, Paul.
>
> 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]
>
> Thanks & regards. =ppy
> --
>
>
>
>
> 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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