Thanks, Jim ... allow me to defer to the NCBO folks to make sense out
of this, and provide us pointers on what to do next (given your
input.) (01)
One thing though .. you said " the process [of the "bioportal_admin"
re-parsing of COSMO ontology] did complete in a about 2 hours despite
the "exception" ... I still see that it shows the state of "Parse
Ontology" on the OOR-sandbox "Browse" screen, and I don't see that
this COSMO ontology can be "explore(d)" yet. (02)
Thanks & regards. =ppy
-- (03)
On Wed, Feb 17, 2010 at 10:20 AM, <jchatign@xxxxxxx> wrote:
> Peter,
>
> As I was putting my slides together for Friday's telcon, I happened to pick
> the COSMO ontology for use with a screen shot. I wanted the "visualize" link
> to be active, so I used bioportal_admin to parse it.
>
> Attached is the relevant messages from the log file. (And a portion of a
> screen shot). There was a Java exception raised during the parsing, but the
> process did complete in a about 2 hours. Perhaps when the parser was invoked
> on the OOR sandbox as a scheduled (cron) job, the exception cause it to
> abort?
>
> Anyway, I thought this info might be helpful.
>
> Jim (04)
>> -----Original Message-----
>> From: Paul R Alexander [mailto:palexander@xxxxxxxxxxxx]
>> Sent: Wednesday, February 17, 2010 7:56 AM
>> To: Peter Yim
>> Cc: OpenOntologyRepository-development
>> Subject: Re: [oor-dev] Parsing Ontologies [was - Fwd:
>> registration... oorsandbox (v2.x)]
>>
>>
>> Peter,
>>
>> 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.
>>
>> Paul (05)
>> 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
>> >
>>
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> (06)
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