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

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

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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