Thanks to all!. I did neglect to mention that I had started with
Tejas, who said ask at oor-users. So now it's full circle. (01)
On Fri, Dec 10, 2010 at 7:00 PM, Peter Yim <peter.yim@xxxxxxxx> wrote:
> Thank you VERY much, Paul, for the prompt response.
>
> There, Bob, your "TDWG-TC" OOR entry is ready.
>
> May I, then, request Tejas (from the NEU team) to help trigger the
> re-parse as necessary, please.
>
> Thanks & regards. =ppy
> --
>
>
> On Fri, Dec 10, 2010 at 3:25 PM, Paul R Alexander
> <palexander@xxxxxxxxxxxx> wrote:
>>
>> Sorry, forgot to mention that anyone with an admin account can manually
>flush the cache at this url:
>> http://oor-01.cim3.net/admin
>>
>> Paul R Alexander
>> Web / UI Developer
>> NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>
>
>> On 12/10/10 3:24 PM, Paul R Alexander wrote:
>>
>> (a) Parsing is done serially on a per-load scheduler run. The load scheduler
>checks for new, unparsed ontologies whenever it is run (we run it every hour,
>I'm not sure how OOR is configured). Nothing should ever get stuck.
>>
>> It looks like maybe the server was rebooted in the middle of a load
>scheduler run or something, which then caused these 02/12/2010 ontologies to
>remain in "parsing" status. This status would mean that they were never
>processed again. You may be able to use the admin tool to trigger a re-parse
>or go into the ncbo_ontology_load_queue table in the database and manually set
>the status column to 1 for these ontologies.
>>
>> (b) If it's a large ontology (500,000+ terms) it could take 6-8 hours to
>process, but anything up to 100,000 terms should process in under an hour,
>usually much faster. Again, nothing should ever be in "parsing" status for too
>long, it should error out at some point and get the "error" status set.
>>
>> (c) I would give up after 24 hours or less depending on the ontology size.
>>
>> Finally, please keep in mind that the UI does aggressive caching. We don't
>expect the system to respond in real-time to many events and as such will
>often cache results for 4-8 hours. For example, the ontology uploaded today
>has actually finished parsing, it's just that the UI hasn't refreshed the
>information.
>> http://oor-01.cim3.net:8080/bioportal/ontologies/10187 shows statusId 3
>("ready")
>> http://oor-01.cim3.net/visualize/10187
>>
>> Cache timeouts can be modified in this file on the UI:
>> /app/models/data_access.rb
>>
>> Paul R Alexander
>> Web / UI Developer
>> NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>
>
>> On 12/10/10 3:00 PM, Peter Yim wrote:
>>
>> Thank you for the input, Bob. ...
>>
>> Let find out from our friends on the BioPortal team (whose technology
>> we are employing in the current OOR-sandbox instance),
>>
>> (a) on whether "parsing" is queued and done serially, or whether they
>> are dealt with in parallel (so that ontologies with errors that are
>> "stuck" in "parsing" aren't block subsequent uploads.)
>>
>> (b) for recommendations on how one should deal with those they are
>> "stuck" at "Parsing Ontology" for a long time.
>>
>> (c) .... and, by the way, when should one consider giving up?2 days?
>> 14 days? 30 days? ... we probably all know that those from 02/12/2010
>> have little chance of making it to the finish. :-)
>>
>> ... Misha? ( ... Paul? ... Natasha?)
>>
>> Thanks & regards. =ppy
>> --
>
>
>> ---------- Forwarded message ----------
>> From: Bob Morris <morris.bob@xxxxxxxxx>
>> Date: Fri, Dec 10, 2010 at 2:27 PM
>> Subject: [oor-users] new ontology stuck(?) behind parse queue
>> To: oor-users@xxxxxxxxxxxxxxxx
>>
>>
>> Around 4 hours ago, I uploaded a new ontology to the sandbox, whose
>> status remains "Waiting to parse". Apparently ahead of it are about 10
>> ontologies uploaded 02/12/2010 (sic!) whose status is "Parsing
>> Ontology". Are those keeping mine from getting parsed, and if so,
>> what should I do about it?
>>
>> Thanks
>> Bob Morris
>>
>>
>> --
>> Robert A. Morris
>> Emeritus Professor of Computer Science
>> UMASS-Boston
>> 100 Morrissey Blvd
>> Boston, MA 02125-3390
>> Associate, Harvard University Herbaria
>> email: morris.bob@xxxxxxxxx
>> web: http://bdei.cs.umb.edu/
>> web: http://etaxonomy.org/mw/FilteredPush
>> http://www.cs.umb.edu/~ram
>> phone (+1) 857 222 7992 (mobile)
>
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> (02)
--
Robert A. Morris
Emeritus Professor of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390
Associate, Harvard University Herbaria
email: morris.bob@xxxxxxxxx
web: http://bdei.cs.umb.edu/
web: http://etaxonomy.org/mw/FilteredPush
http://www.cs.umb.edu/~ram
phone (+1) 857 222 7992 (mobile) (03)
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