Re: [XMLPipeDB-developer] GM Builder 2.0b66 verification underway

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

FYI,

wip 486 Database Systems report here:
https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=User:Rbrousla#Overview

Starts at Section 1.2, added link to SCCUR 2011 as well.

More GDB testing analysis to come shortly.

Richard



On Tue, Dec 20, 2011 at 4:04 PM, John David N. Dionisio <do...@lm...>wrote:

> Greetings,
>
> Thanks for the updates.  I agree that a close review of the tally engine
> configuration is called for (I believe this is in gmbuilder.properties).
>  The tally engine code should also be revisited to see if its PostgreSQL
> queries filter for the specific taxon ID of the individual species.
>
> Because XML files are still single-species, it may be that we can only do
> tallies one species at a time.  Ideally, the tally engine reads the taxon
> ID from the XML file, then passes it on to the database portion so that the
> database queries can then include that taxon ID as part of the query filter.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Associate Director, University Honors Program
> Loyola Marymount University
>
>
>
> On Dec 20, 2011, at 11:17 AM, Richard Brous wrote:
>
> > Additionally:
> >
> > Could also be the Mtuber xml source that is causing problems for tally
> engine which also could be affected by the profile customization...
> >
> > More later after I spend some cycles on IxD.
> >
> > RB
> >
> > On Tue, Dec 20, 2011 at 10:35 AM, Richard Brous <rbr...@gm...>
> wrote:
> > 12/19/2011 - 12/20/2011
> >
> > Mycobacterium smegmatis
> > Created new single species GDB and Postgre db (from latest downloaded
> source)
> > Verified with Tally Engine that all xml tags were imported into Postgre
> as records (attached ss)
> > GDB file size 25,824KB
> >
> > Mycobacterium tuberculosis H37Rv
> > Created new single species GDB and Postgre db (from latest downloaded
> source)
> > Tally Engine verifies that there is an issue with Ordered Locus: wrong
> count and Ordered Locus listed twice (attached ss)
> > GDB  file size 23,404KB
> >
> > Msmeg and Mtuber dual species GDB and Postgre db created from above
> source (go-obo imported and processed only once)
> > Tally Engine screen shots of both species compared to total records
> (need to rethink tally engine implementation?)
> > single species Msmeg GDB export file size 20,580KB (much smaller, likely
> missing records!!!)
> > single species Mtuber GDB export file size 23,404KB (identical byte size)
> >
> >
> > NEXT STEPS:
> >
> > Msmeg
> > Compare GDB tables from single species db export and two species db
> export (expect to find records or something missing)
> > Verify record counts in Postgre db by SQL queries
> > Verify no Mtuber records were exported into Msmeg GDB
> >
> > Mtuber
> > Tally engine error only occurs with Mt, so likely something to do with
> the profile customization (tally engine code works fine with Ms)
> > Verify record counts in Postgre db by SQL queries
> > Verify no Msmeg records were exported into Mtuber GDB
> >
> > ONCE ABOVE SOLVED
> >
> > 1. Export Msmeg and Mtuber into 2 species GDB and ensure all records for
> each species exist
> > 2. Introduce a third species into Postgre to ensure that if its not
> selected, it isn't exported
> >
> >
> >
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
>
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