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

[John D. N. D. <do...@lm...>]

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>