Re: [XMLPipeDB-developer] 499 - PROBLEM - M tuberculosis xml tag importation

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

OK, so based on your approach:

1. I'll start with reviewing the queries for xmlpipedb-match and sql queries
needed for the respective results as you requested.

I was also thinking I may need to review the schema from xml into postgres
but the issue isn't likely a schema error. The error most likely lies in how
xmlpipedbutils queries the data from xml source and writes to the
tables what it returns?

2. I'll review the code: trace the entrance of tally engine in the gmbuilder
code then follow it through the xmlpipedbutils.

Richard

On Sat, Feb 5, 2011 at 10:28 AM, John David N. Dionisio <do...@lm...>wrote:

> Just wanted to confirm (since I wasn't sure in the first e-mail) --- the
> XMLPipeDB Utilities source code is in trunk/xmlpipedbutils in SourceForge's
> Subversion repo.
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
> On Feb 5, 2011, at 10:02 AM, Richard Brous wrote:
>
>  > Hi Dondi,
> >
> > So I'm at the point in working with M tuberculosis that I was able to
> exactly reproduce Dr. Dahlquist's problematic TallyEngine results.
> >
> > gmb2b60 Results
> >
> >
> >
> > Now the proverbial question - What next to solve the Ordered Locus
> import/count issue?
> >
> > **********************************************
> > Here is my thought process:
> >
> > Step 1: How does the import process work at the high level? (obviously
> correct me if I'm wrong)
> >
> > I believe that basically as each XML tag is read, it is placed in the
> proper Postgres table(s) based on some criteria. There is also likely some
> sort of check that each individual tag is in valid XML format unless we
> don't care at this stage (care at export) or maybe the parser just skips
> over and goes on to the next .
> >
> > Step 2: What could be the problem?
> >
> > Either -
> > a. XML tags are being parsed incorrectly (ignored/skipped)?
> > b. Decision criteria of which table they should be added to?
> >
> > **********************************************
> >
> > I read on the sourceforge wiki:
> >
> > XMLPipeDB has a modular architecture with three components that may be
> used separately or together. XSD-to-DB reads an XSD (XML Schema Definition)
> and automatically generates an SQL schema, Java classes, and Hibernate
> mappings. XMLPipeDB Utilities provides functionality for configuring the
> database, importing data, and performing queries. GenMAPP Builder is based
> on the XMLPipeDB Utilities and exports GenMAPP-compatible Gene Databases
> based on data from UniProt and Gene Ontology (GO).
> >
> > So I should probably start with the XMLPipeDB Utilities which are where?
> I don't see any in the basic distribution or are they not standalone and
> called from the command line?
> >
> > Thanks!
> >
> > Richard
>
>