Thank you VERY much, Paul, for the prompt response. (01)
There, Bob, your "TDWG-TC" OOR entry is ready. (02)
May I, then, request Tejas (from the NEU team) to help trigger the
re-parse as necessary, please. (03)
Thanks & regards. =ppy
-- (04)
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 (05)
> 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 (06)
> 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
> -- (07)
> ---------- 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) (08)
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