Peter, (01)
It sounds like there was a failure at some point during the ontology
parsing process, meaning that the process had started, setting the
ontology status to "Parsing", but never finished, so the ontology status
was never updated. There is a "Parsing Error" status, I'm not sure why
that wasn't set if a problem was encountered. I would try to login to
the BioPortal Admin software and trigger a re-parse on Pat's ontology.
If it does encounter an error during the process, the Admin UI should
report that back to you. (02)
Paul (03)
On 2/17/10 8:41 AM, Peter Yim wrote:
> Paul or Someone from NCBO who might point us in the right direction ...
>
> Further to the earlier exchange with PatCassidy (below), looks like
> his COSMO ontology (which Pat uploaded on 2010.02.11) is still "being
> parsed" at the OOR-Sandbox (v2.x).
>
> (Not knowing what exactly to look for) I just went into the server and
> check cpu workload on the<oor-01> vm. To my surprise, the cpu(s) is
> running at 99.5% to 100% idle. ... I do notice that 19 (of the 116)
> ontologies that are listed in the "Browse" page are supposed to be in
> the state of "Parse Ontology." ... therefore, this doesn't sound
> right!
>
> ... Suggestions?
>
> Thanks& regards. =ppy
> --
>
>
> ---------- Forwarded message ----------
> From: Patrick Cassidy<pat@xxxxxxxxx>
> Date: Fri, Feb 12, 2010 at 7:31 PM
> Subject: RE: registration problem oor sandbox (v2.x)
> To: Peter Yim<peter.yim@xxxxxxxx>
> Cc: Tejas Parikh<tejas@xxxxxxxxxxxxxxx>, Paul R Alexander
> <palexander@xxxxxxxxxxxx>, Ken Baclawski<kenb@xxxxxxxxxxx>, "Obrst,
> Leo J."<lobrst@xxxxxxxxx>, Mike Dean<mdean@xxxxxxx>
>
>
> On the parsing time for the new sandbox:
>
>>
>>> [PatC] Any idea how long a 7000 element ontology should take to
>>>
>> parse?
>>
>> [ppy] (I'm guessing, but) I don't think anyone knows* ... Please make
>> a note on how long it is taking this time for COSMO, maybe when you
>> are done, you can share the experience with all of us. [ *since
>> different installs are running on fairly different hardware and
>> platforms, and experiencing different work loads all the time. ]
>>
> The COSMO is still "parsing" after over 24 hours. I see a parsing error for
> the OWL-time ontology (didn't see that in the last version). Who is
> maintaining the parser and display function? Any thoughts on how this can
> be improved?
>
> The "explore" function is really valuable. I hope we can get it to be
> consistently effective. Sorry I have no programming expertise to help out
> here.
>
> Pat
>
> Patrick Cassidy
> MICRA, Inc.
> 908-561-3416
> cell: 908-565-4053
> cassidy@xxxxxxxxx
> (04)
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