Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b65 has been released

[Kam D. <kda...@lm...>]

Hi,

Ah.  So I think what happened is the same thing with E. coli, they 
made an ID for a more specific strain (in this case S288c) because 
they are sequencing more substrains of yeast.

I think option 1 below is the way to go.  Can't we discover what the 
name is by reading the xml?

Thanks,
Kam

At 10:53 PM 11/1/2011, John David N. Dionisio wrote:
>Greetings,
>
>I checked the S. cerevisiae species profile in the code and its 
>Taxon ID is 4932.  Thus, you were indeed seeing a generic species 
>profile being called up to do this export because the included yeast 
>profile did not have a matching Taxon ID.
>
>I can change the profile to use 559292 no problem.  However, this 
>scenario still reveals a bug for when the generic species profile is 
>invoked: the species name becomes null, and code that processes this 
>name crashes on that condition.
>
>For this latter issue, there are two ways to fix it:
>
>- Make the generic species profile still provide some kind of 
>species name (or make the user enter one?).
>- Make the export code more robust by not crashing in the case where 
>the species name is null.
>
>I'm thinking that the former is the right way to go (the species 
>name is used to offer a default filename for the GDB, as well as for 
>various columns in the GDB schema, so its being null or blank may 
>cause issues in that aspect).
>
>John David N. Dionisio, PhD
>Associate Professor, Computer Science
>Associate Director, University Honors Program
>Loyola Marymount University
>
>
>On Nov 1, 2011, at 4:32 PM, Kam Dahlquist wrote:
>
> > This time with attachments.
> >
> > At 04:31 PM 11/1/2011, Kam Dahlquist wrote:
> >> Hi,
> >>
> >> I finally had a chance to try a yeast export wtih GMB2.0b65--I
> >> didn't get very far:
> >>
> >> 1.  I imported the UniProt, GO, and GOA all fine.  When I started
> >> the export, the Species panel listed "Taxon ID 559292,
> >> null".  That's the correct taxon ID for the species I am
> >> importing/exporting, but shouldn't it also tell me the species name,
> >> not just null?  or is that what happens when the generic profile is
> >> called.  There should be a Saccharomyces cerevisiae profile in
> >> GenMAPP Builder somewhere, even though we never finished it.
> >>
> >> 2.  In the next window, I click on the box "Save GenMAPP Database
> >> File As..." and nothing happens.  Screenshots of the console window
> >> (parts 1 and 2, could not fit into one screen) are attached.
> >>
> >> 3.  The title bar and notes field of the export wizard did not get
> >> updated to gmb2.0b65.
> >>
> >> Thanks,
> >> Kam
> >>
> >> At 11:13 PM 10/14/2011, you wrote:
> >>> GenMAPP Builder 2.0b65 Release Notes
> >>>
> >>> This release of GenMAPP Builder includes a preliminary
> >>> implementation of multi-species Gene Database exports, as well as
> >>> user interface changes to the export wizard.  This version also
> >>> updates the Gene Ontology database library to accommodate the
> >>> latest elements included in GO OBO XML downloads.
> >>>
> >>>
> >>> 
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