Re: [XMLPipeDB-developer] UniProtDatabaseProfile submits

[Richard B. <rbr...@gm...>]

roger, thanks.

richard

On Fri, Sep 2, 2011 at 11:10 AM, John David N. Dionisio <do...@lm...>wrote:

> OK, thanks.  I will look into issue #1 concurrently and will report back.
>  Regarding issue #2, I confirmed with Kam that we do need the per-species
> value for each ID.  As we are prioritizing database approaches first, here
> you have a distinct exercise in SQL formation that is relevant to the
> tutorial course:
>
> - Modify the formed query so that it returns, for each ID, the
> corresponding species name.  If successful, you will then have both ID and
> species name to provide to tableManager.submit, and you will not need an
> outer loop for every species profile.
>
> The way I suggest you do this is to form a valid query directly in
> PostgreSQL (i.e., via pgAdmin or psql).  That should be pretty easy to get
> since you are logging the final query string --- just copy and paste that.
>  Experiment with the query directly within PostgreSQL until you have one
> that works.  Then transplant that into the code.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Associate Director, University Honors Program
> Loyola Marymount University
>
>
>
> On Sep 2, 2011, at 11:04 AM, Richard Brous wrote:
>
> > OK, so still two outstanding issues regarding the last 2 modified
> methods:
> >
> > 1. getInfoTableManager()
> >
> > Still returning 3 species names when only two are selected. Returns one
> species name when only one is selected.
> > - I will review the loop again and see if I can determine what is going
> on here.
> >
> > 2. getSystemTableManager()
> >
> > I added a for loop within the while condition which after discussions we
> know is incorrect. Will pull that out but we need to determine how to move
> forward with the issue of determining which species each id belongs to.
> removed loop and submitted to SourceForge but now build is essentially
> broken till we figure out the wrinkle. Adding a for speciesprofile loop at
> the top was discussed as a solution of last resort.
> >
> > UniProtDatabaseProfile - while loop begins at line # 585
> >
> >
> ---------------------------------------------------------------------------------------------------------------
> >
> > Also made modifications to getSystemsTableManager() which applies the
> species customizations for each species profile selected. Seems correct to
> me but please confirm.
> >
> >
> --------------------------------------------------------------------------------------------------------------
> >
> > Discussions surrounding getPrimarySystemTableManager() assumed likely bad
> coding since it seems to call for a customized schema although it is
> identical to the default UniProt schema.
> >
> > It calls getPrimarySystemTableManagerCustomizations() which is specific
> to Arabidopsis thaliana and Ecoli only.
> >
> > Didn't want to dig into this yet until other higher priority
> modifications were done first plus I believe a discussion with Dr. D was
> going to occur as well.
> >
> >
> ---------------------------------------------------------------------------------------------------------------
> >
> > getRelationsTableManager() is the last method which remains untouched but
> I will start reviewing and come up with a plan of attack.
> >
> >
> --------------------------------------------------------------------------------------------------------------
> >
> > These are all the loose ends I can think of to document.
> >
> > Thanks!
> >
> > Richard
> >
> >
> >
> > On Wed, Aug 31, 2011 at 12:52 PM, Richard Brous <rbr...@gm...>
> wrote:
> > Submitted changes to UniProtDatabaseProfile based on the logical
> corrections from yesterdays convo with Dondi.
> >
> > These do not yet include the discussed optimizations, just wanted to get
> it working and do some test exports... which completed successfully.
> >
> > I also added a for loop under the while loop in getSystemTableManager()
> to ensure each query result is processed for each selected species profile.
> > The loop is on line 587 and I added it because it seemed a solution to
> have each species profile included... is this correct or should I be
> submitting all at once versus each species?
> >
> > Richard
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
>
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