xmlpipedb-developer — Mailing list for XMLPipeDB software development questions and discussions.

Re: [XMLPipeDB-developer] gmb2b71 crash during export of Vibrio

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

This is a pretty low-level error...I'd say the first step in triaging it is to gather up versions: what version of Windows is your machine running, and what version of PostgreSQL?  Java can be seen here (6.0_43-b01).

The Keck lab computers on which students have been doing their exports have Windows 7, Java 7u45, and PostgreSQL 9.2.4.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Nov 22, 2013, at 4:29 PM, Kam Dahlquist <kda...@lm...> wrote:

> Hi,
> 
> My attempted export of Vibrio with gmb2b71 crashed.  I'm attaching a screenshot of the console window.  I tried to upload it to the wiki, but also got an error there:
> 
> 	• Could not acquire lock for "mwstore://local-backend/local-public/4/43".
> 	• Could not acquire lock for "mwstore://local-backend/local-public/4/43/Gmb2b71_crash_20131122.jpg".
> 
> I'm going to try an export of H. pylori, if I can get it started before I leave on a different computer, although I have to get it started in the next 15 min...
> 
> Kam
> <gmb2b71_crash_20131122.jpg>------------------------------------------------------------------------------
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[XMLPipeDB-developer] H pylori generic profile issue gmb2b71

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

Hi,

Just started an export of H. pylori.  There were two profiles that 
showed up, both with the same taxon ID, both said they were generic 
profiles.  I'm attaching 2 screenshots.

Best,
Kam

[XMLPipeDB-developer] gmbuilder 2.0b67 with multi-species export has been released on sourceforge.

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

The default download updated to this latest version.

Thank you.

Richard

Re: [XMLPipeDB-developer] CMSI 486T up on the Sourceforge wiki ready for review and comments

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

Sounds good, I will take a look and let you know.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Jan 5, 2012, at 5:46 PM, Richard Brous wrote:

> Please take a look at the detailed report when able.
> 
> Are details in line with your expectations or am I missing anything based on the SCCUR changes to deliverables?.
> 
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=User:Rbrousla
> 
> Thanks!
> 
> Richard
> <ATT00001..txt><ATT00002..txt>

[XMLPipeDB-developer] CMSI 486T up on the Sourceforge wiki ready for review and comments

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

Please take a look at the detailed report when able.

Are details in line with your expectations or am I missing anything based
on the SCCUR changes to deliverables?.

https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=User:Rbrousla

Thanks!

Richard

Re: [XMLPipeDB-developer] Multi-species GMBuilder testing info at link below

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

Hi Dondi,

Yes the idea was to compare the original row count values of the Combined
GDB to the sum of the original row count values of each Single Species GDB.

I updated the spreadsheet for clarity so I hope it makes more sense when
reviewed.

In regard to spreadsheet comments, the sharing of GO terms made sense to me
but the InterPro and Pfam results did not.

But my assumption of InterPro and Pfam being another full gene id system
was incorrect...

   - InterPro is a db of protein signatures which likely doesn't have
   1:1 correspondence to the Ordered Locus IDs
   - Pfam is a db of protein multiple sequence alignment and profile hidden
   Markov models which also doesn't likely have a 1:1 correspondence to the
   Ordered Locus IDs.

So I withdraw my questions and submit that the Ms-Mt combined GDB in fact
is OK. Of course Dr. D still has to weigh in on the matter =D

Richard

On Mon, Jan 2, 2012 at 2:06 AM, John David N. Dionisio <do...@lm...>wrote:

> Hi Rich,
>
> Thank you for the updates.  There's been quite a bit of information to
> absorb, but that last wiki page really helped to sum things up.  Things
> look OK to me; on the combined export, what precisely do the "combined
> rows" and "individs added" columns mean?  My guess is that "combined rows"
> is the actual number of rows found, while "individs added" is the sum of
> what you found for each individual species. It seems, then, that your
> questions on the InterPro and Pfam rows hint at strong overlap between IDs
> from the two species.  Am I understanding the numbers and your questions
> correctly?
>
> If so, then it seems that the course of investigation would be to identify
> the overlapping IDs (i.e., IDs that are in both individual species records)
> then count them up to see if they make up the difference.  You can probably
> hit either the PostgreSQL database or the original XML files; what would
> vary would be the tools you would use (SQL in the former, assorted text
> processing commands in the latter).
>
> The above course of action is based on whether I understand the issue, so
> please see first if what I've written lines up with your thoughts, or if
> further explanation is required.
>
> The other data look good though --- nice to see things line up well
> otherwise!
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Associate Director, University Honors Program
> Loyola Marymount University
>
>
>
> On Jan 1, 2012, at 9:23 PM, Richard Brous wrote:
>
> > The GDB testing results have been updated (and corrected in some cases)
> and placed on wiki.
> >
> > Please review and provide feedback when able.
> >
> >
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=GDB_Verification_and_Testing
> >
> > Thank you!
> >
> > Richard
> >
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Re: [XMLPipeDB-developer] Multi-species GMBuilder testing info at link below

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

Hi Rich,

Thank you for the updates.  There's been quite a bit of information to absorb, but that last wiki page really helped to sum things up.  Things look OK to me; on the combined export, what precisely do the "combined rows" and "individs added" columns mean?  My guess is that "combined rows" is the actual number of rows found, while "individs added" is the sum of what you found for each individual species. It seems, then, that your questions on the InterPro and Pfam rows hint at strong overlap between IDs from the two species.  Am I understanding the numbers and your questions correctly?

If so, then it seems that the course of investigation would be to identify the overlapping IDs (i.e., IDs that are in both individual species records) then count them up to see if they make up the difference.  You can probably hit either the PostgreSQL database or the original XML files; what would vary would be the tools you would use (SQL in the former, assorted text processing commands in the latter).

The above course of action is based on whether I understand the issue, so please see first if what I've written lines up with your thoughts, or if further explanation is required.

The other data look good though --- nice to see things line up well otherwise!

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Jan 1, 2012, at 9:23 PM, Richard Brous wrote:

> The GDB testing results have been updated (and corrected in some cases) and placed on wiki.
> 
> Please review and provide feedback when able.
> 
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=GDB_Verification_and_Testing
> 
> Thank you!
> 
> Richard
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual 
> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox_______________________________________________
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[XMLPipeDB-developer] Multi-species GMBuilder testing info at link below

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

The GDB testing results have been updated (and corrected in some cases) and
placed on wiki.

Please review and provide feedback when able.

https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=GDB_Verification_and_Testing

Thank you!

Richard

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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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>

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

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

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
>
>
>
>
>

Re: [XMLPipeDB-developer] GenMAPP Builder 2.0 Beta 66 Released

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

Greetings,

OK, I can make those UI changes.  I will also look into restoring the "export" folder functionality and appending "External" to the default gdb name.

In terms of a species export request...the main one I can think of is to see how a generic export goes (i.e., a species for which we have not created a custom profile).  Also, if things look encouraging, perhaps we can test a MRSA export too?

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Nov 9, 2011, at 4:37 PM, Kam Dahlquist wrote:

> Hi,
> 
> I was able to successfully export a yeast gdb using this build.  I 
> haven't had a chance to analyze the results, though.
> 
> A couple of interface things that drew my attention:
> 
> 1.  On the first screen of the export wizard, I find that I don't 
> realize that I have to click on the species name to activate the 
> "Next" button.  Even though I should supposedly know how this works, 
> it takes me a moment to know what to do.  I think this is because 
> only one species is showing.  However, maybe on the left it could say 
> something like, "Choose which species to export" or "Click on the 
> species you wish to export" or something like that.
> 
> 2.  On the second export screen, previously when you clicked on the 
> save button, it automatically created a folder named "export" within 
> the gmb folder to hold the gdb's.  This functionality appears to be 
> gone with the new interface.
> 
> 3.  I can't remember if we discussed this, but I was wondering if we 
> could insert the word "External" into the default gdb name, as in 
> "Pf-Std_External_20090604.gdb" for example.
> 
> I'll let you know when I get a chance to analyze the data.
> 
> Are there any requests for particular species' exports that you guys 
> would like me to check in particular?
> 
> Thanks,
> Kam
> 
> At 10:27 AM 11/7/2011, you wrote:
>> GenMAPP Builder 2.0 Beta 66 has been released.  This release of 
>> GenMAPP Builder includes an important fix in the implementation of 
>> multi-species Gene Database exports and improvements on how the 
>> species name is determined and assigned.  The taxon ID for the 
>> Saccharomyces cerevisiae species profile was also changed to 559292.
>> ------------------------------------------------------------------------------
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> 
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Re: [XMLPipeDB-developer] GenMAPP Builder 2.0 Beta 66 Released

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

Hi,

I was able to successfully export a yeast gdb using this build.  I 
haven't had a chance to analyze the results, though.

A couple of interface things that drew my attention:

1.  On the first screen of the export wizard, I find that I don't 
realize that I have to click on the species name to activate the 
"Next" button.  Even though I should supposedly know how this works, 
it takes me a moment to know what to do.  I think this is because 
only one species is showing.  However, maybe on the left it could say 
something like, "Choose which species to export" or "Click on the 
species you wish to export" or something like that.

2.  On the second export screen, previously when you clicked on the 
save button, it automatically created a folder named "export" within 
the gmb folder to hold the gdb's.  This functionality appears to be 
gone with the new interface.

3.  I can't remember if we discussed this, but I was wondering if we 
could insert the word "External" into the default gdb name, as in 
"Pf-Std_External_20090604.gdb" for example.

I'll let you know when I get a chance to analyze the data.

Are there any requests for particular species' exports that you guys 
would like me to check in particular?

Thanks,
Kam

At 10:27 AM 11/7/2011, you wrote:
>GenMAPP Builder 2.0 Beta 66 has been released.  This release of 
>GenMAPP Builder includes an important fix in the implementation of 
>multi-species Gene Database exports and improvements on how the 
>species name is determined and assigned.  The taxon ID for the 
>Saccharomyces cerevisiae species profile was also changed to 559292.
>------------------------------------------------------------------------------
>RSA(R) Conference 2012
>Save $700 by Nov 18
>Register now
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Re: [XMLPipeDB-developer] GenMAPP Builder 2.0 Beta 66 Released

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

Looking good, can see both species listed under ordered locus names which
was a previously documented issue.

Will do a more comprehensive export review once I get the next round of the
sccur ppt done.

Richard

On Mon, Nov 7, 2011 at 10:30 AM, Richard Brous <rbr...@gm...> wrote:

> Great! Will pull it down to start a few tests of my own.
>
> Richard
>
>
> On Mon, Nov 7, 2011 at 10:27 AM, John David N. Dionisio <do...@lm...>wrote:
>
>> GenMAPP Builder 2.0 Beta 66 has been released.  This release of GenMAPP
>> Builder includes an important fix in the implementation of multi-species
>> Gene Database exports and improvements on how the species name is
>> determined and assigned.  The taxon ID for the Saccharomyces cerevisiae
>> species profile was also changed to 559292.
>>
>> ------------------------------------------------------------------------------
>> RSA(R) Conference 2012
>> Save $700 by Nov 18
>> Register now
>> http://p.sf.net/sfu/rsa-sfdev2dev1
>> _______________________________________________
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>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>
>
>

Re: [XMLPipeDB-developer] GenMAPP Builder 2.0 Beta 66 Released

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

Great! Will pull it down to start a few tests of my own.

Richard

On Mon, Nov 7, 2011 at 10:27 AM, John David N. Dionisio <do...@lm...>wrote:

> GenMAPP Builder 2.0 Beta 66 has been released.  This release of GenMAPP
> Builder includes an important fix in the implementation of multi-species
> Gene Database exports and improvements on how the species name is
> determined and assigned.  The taxon ID for the Saccharomyces cerevisiae
> species profile was also changed to 559292.
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
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>

[XMLPipeDB-developer] GenMAPP Builder 2.0 Beta 66 Released

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

GenMAPP Builder 2.0 Beta 66 has been released.  This release of GenMAPP Builder includes an important fix in the implementation of multi-species Gene Database exports and improvements on how the species name is determined and assigned.  The taxon ID for the Saccharomyces cerevisiae species profile was also changed to 559292.

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

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

Greetings,

Yes, the missed section (method) is UniProtDatabaseProfile.getPrimarySystemTableManager.  If you look at the current commit, you will see that it still uses only the first species profile in the selected collection.  The other methods have been duly tweaked, and as far as I can tell look largely OK.

I've done a couple of exports at this point, and found some things to tweak with each one, but I think I am at a point where I can commit then release soon.  I have just one more export in progress to verify the latest changes, then I'll stop there.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Nov 6, 2011, at 10:28 AM, Richard Brous wrote:

> Interesting, what missed section??!!
> 
> Look forward to the new build so I can do some testing on my own.
> 
> 
> Richard
> 
> On Sun, Nov 6, 2011 at 12:15 AM, John David N. Dionisio <do...@lm...> wrote:
> Greetings,
> 
> I just wanted to post an update that a new build (2.0b66) will be on its way in a day or so.  I'm just waiting for a test export run to conclude then will proceed based on how that goes.
> 
> This build will have the right taxon ID for S. cerevisiae, will supply a species name if the generic species profile is used (i.e., selected species does not have a custom profile), and, finally, may address the bug that Rich as reported about a single ID only appearing in a supposed multi-species export.
> 
> The first two fixes are relatively straightforward and easy to confirm without doing a full export, but the last one needs the export for confirmation.  The issue with this is that there was actually a step that got overlooked in the "multiple species" transition.  I was in a holding pattern with that for so long because I had focused in the sections that Rich had changed, thinking that there may be a bug there, when it may turn out that the issue was in something that was actually *not* changed in his last round of commits (and thus it did not go under the microscope until I finally stepped a little further back to see what was going on through the overall export process).
> 
> Anyway, we will see after this export whether I was barking up the right tree.  Stay tuned  :)
> 
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Associate Director, University Honors Program
> Loyola Marymount University
> 
> 
> On Nov 2, 2011, at 4:33 PM, Kam Dahlquist wrote:
> 
> > Hi,
> >
> > Yes, sorry, that is the correct taxon ID and it should be changed.
> >
> > Best,
> > Kam
> >
> > At 04:16 PM 11/2/2011, you wrote:
> >> Yes, a query for the name should be doable.  It will be a matter of
> >> finding the right time/place to do it.
> >>
> >> Also, just to confirm, should the taxon ID be changed then to 559292?
> >>
> >> John David N. Dionisio, PhD
> >> Associate Professor, Computer Science
> >> Associate Director, University Honors Program
> >> Loyola Marymount University
> >>
> >>
> >>
> >> On Nov 2, 2011, at 8:41 AM, Kam Dahlquist wrote:
> >>
> >>> 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.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>
> >> ------------------------------------------------------------------------------
> >>>>>>> All the data continuously generated in your IT infrastructure
> >> contains a
> >>>>>>> definitive record of customers, application performance, security
> >>>>>>> threats, fraudulent activity and more. Splunk takes this data and makes
> >>>>>>> sense of it. Business sense. IT sense. Common sense.
> >>>>>>> http://p.sf.net/sfu/splunk-d2d-oct
> >>>>>>> _______________________________________________
> >>>>>>> xmlpipedb-developer mailing list
> >>>>>>> xml...@li...
> >>>>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>> <Save_error_1.jpg><Save_error_2.jpg><ATT00001..txt><ATT00002..txt>
> >>>>
> >>>>
> >>>>
> >> ------------------------------------------------------------------------------
> >>>> RSA&#174; Conference 2012
> >>>> Save $700 by Nov 18
> >>>> Register now&#33;
> >>>> http://p.sf.net/sfu/rsa-sfdev2dev1
> >>>> _______________________________________________
> >>>> xmlpipedb-developer mailing list
> >>>> xml...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>
> >>>
> >>>
> >> ------------------------------------------------------------------------------
> >>> RSA&#174; Conference 2012
> >>> Save $700 by Nov 18
> >>> Register now&#33;
> >>> http://p.sf.net/sfu/rsa-sfdev2dev1
> >>> _______________________________________________
> >>> xmlpipedb-developer mailing list
> >>> xml...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>
> >>
> >> ------------------------------------------------------------------------------
> >> RSA(R) Conference 2012
> >> Save $700 by Nov 18
> >> Register now
> >> http://p.sf.net/sfu/rsa-sfdev2dev1
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> > ------------------------------------------------------------------------------
> > RSA(R) Conference 2012
> > Save $700 by Nov 18
> > Register now
> > http://p.sf.net/sfu/rsa-sfdev2dev1
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> 
> 
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> 
> <ATT00001..txt><ATT00002..txt>

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

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

Interesting, what missed section??!!

Look forward to the new build so I can do some testing on my own.


Richard

On Sun, Nov 6, 2011 at 12:15 AM, John David N. Dionisio <do...@lm...>wrote:

> Greetings,
>
> I just wanted to post an update that a new build (2.0b66) will be on its
> way in a day or so.  I'm just waiting for a test export run to conclude
> then will proceed based on how that goes.
>
> This build will have the right taxon ID for S. cerevisiae, will supply a
> species name if the generic species profile is used (i.e., selected species
> does not have a custom profile), and, finally, may address the bug that
> Rich as reported about a single ID only appearing in a supposed
> multi-species export.
>
> The first two fixes are relatively straightforward and easy to confirm
> without doing a full export, but the last one needs the export for
> confirmation.  The issue with this is that there was actually a step that
> got overlooked in the "multiple species" transition.  I was in a holding
> pattern with that for so long because I had focused in the sections that
> Rich had changed, thinking that there may be a bug there, when it may turn
> out that the issue was in something that was actually *not* changed in his
> last round of commits (and thus it did not go under the microscope until I
> finally stepped a little further back to see what was going on through the
> overall export process).
>
> Anyway, we will see after this export whether I was barking up the right
> tree.  Stay tuned  :)
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Associate Director, University Honors Program
> Loyola Marymount University
>
>
> On Nov 2, 2011, at 4:33 PM, Kam Dahlquist wrote:
>
> > Hi,
> >
> > Yes, sorry, that is the correct taxon ID and it should be changed.
> >
> > Best,
> > Kam
> >
> > At 04:16 PM 11/2/2011, you wrote:
> >> Yes, a query for the name should be doable.  It will be a matter of
> >> finding the right time/place to do it.
> >>
> >> Also, just to confirm, should the taxon ID be changed then to 559292?
> >>
> >> John David N. Dionisio, PhD
> >> Associate Professor, Computer Science
> >> Associate Director, University Honors Program
> >> Loyola Marymount University
> >>
> >>
> >>
> >> On Nov 2, 2011, at 8:41 AM, Kam Dahlquist wrote:
> >>
> >>> 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.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>
> >>
> ------------------------------------------------------------------------------
> >>>>>>> All the data continuously generated in your IT infrastructure
> >> contains a
> >>>>>>> definitive record of customers, application performance, security
> >>>>>>> threats, fraudulent activity and more. Splunk takes this data and
> makes
> >>>>>>> sense of it. Business sense. IT sense. Common sense.
> >>>>>>> http://p.sf.net/sfu/splunk-d2d-oct
> >>>>>>> _______________________________________________
> >>>>>>> xmlpipedb-developer mailing list
> >>>>>>> xml...@li...
> >>>>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>>> <Save_error_1.jpg><Save_error_2.jpg><ATT00001..txt><ATT00002..txt>
> >>>>
> >>>>
> >>>>
> >>
> ------------------------------------------------------------------------------
> >>>> RSA&#174; Conference 2012
> >>>> Save $700 by Nov 18
> >>>> Register now&#33;
> >>>> http://p.sf.net/sfu/rsa-sfdev2dev1
> >>>> _______________________________________________
> >>>> xmlpipedb-developer mailing list
> >>>> xml...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>
> >>>
> >>>
> >>
> ------------------------------------------------------------------------------
> >>> RSA&#174; Conference 2012
> >>> Save $700 by Nov 18
> >>> Register now&#33;
> >>> http://p.sf.net/sfu/rsa-sfdev2dev1
> >>> _______________________________________________
> >>> xmlpipedb-developer mailing list
> >>> xml...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> RSA(R) Conference 2012
> >> Save $700 by Nov 18
> >> Register now
> >> http://p.sf.net/sfu/rsa-sfdev2dev1
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> >
> ------------------------------------------------------------------------------
> > RSA(R) Conference 2012
> > Save $700 by Nov 18
> > Register now
> > http://p.sf.net/sfu/rsa-sfdev2dev1
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>

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

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

Greetings,

I just wanted to post an update that a new build (2.0b66) will be on its way in a day or so.  I'm just waiting for a test export run to conclude then will proceed based on how that goes.

This build will have the right taxon ID for S. cerevisiae, will supply a species name if the generic species profile is used (i.e., selected species does not have a custom profile), and, finally, may address the bug that Rich as reported about a single ID only appearing in a supposed multi-species export.

The first two fixes are relatively straightforward and easy to confirm without doing a full export, but the last one needs the export for confirmation.  The issue with this is that there was actually a step that got overlooked in the "multiple species" transition.  I was in a holding pattern with that for so long because I had focused in the sections that Rich had changed, thinking that there may be a bug there, when it may turn out that the issue was in something that was actually *not* changed in his last round of commits (and thus it did not go under the microscope until I finally stepped a little further back to see what was going on through the overall export process).

Anyway, we will see after this export whether I was barking up the right tree.  Stay tuned  :)

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University


On Nov 2, 2011, at 4:33 PM, Kam Dahlquist wrote:

> Hi,
> 
> Yes, sorry, that is the correct taxon ID and it should be changed.
> 
> Best,
> Kam
> 
> At 04:16 PM 11/2/2011, you wrote:
>> Yes, a query for the name should be doable.  It will be a matter of 
>> finding the right time/place to do it.
>> 
>> Also, just to confirm, should the taxon ID be changed then to 559292?
>> 
>> John David N. Dionisio, PhD
>> Associate Professor, Computer Science
>> Associate Director, University Honors Program
>> Loyola Marymount University
>> 
>> 
>> 
>> On Nov 2, 2011, at 8:41 AM, Kam Dahlquist wrote:
>> 
>>> 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.
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>> 
>> ------------------------------------------------------------------------------
>>>>>>> All the data continuously generated in your IT infrastructure 
>> contains a
>>>>>>> definitive record of customers, application performance, security
>>>>>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>>>>>> sense of it. Business sense. IT sense. Common sense.
>>>>>>> http://p.sf.net/sfu/splunk-d2d-oct
>>>>>>> _______________________________________________
>>>>>>> xmlpipedb-developer mailing list
>>>>>>> xml...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>>>> <Save_error_1.jpg><Save_error_2.jpg><ATT00001..txt><ATT00002..txt>
>>>> 
>>>> 
>>>> 
>> ------------------------------------------------------------------------------
>>>> RSA&#174; Conference 2012
>>>> Save $700 by Nov 18
>>>> Register now&#33;
>>>> http://p.sf.net/sfu/rsa-sfdev2dev1
>>>> _______________________________________________
>>>> xmlpipedb-developer mailing list
>>>> xml...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>> 
>>> 
>>> 
>> ------------------------------------------------------------------------------
>>> RSA&#174; Conference 2012
>>> Save $700 by Nov 18
>>> Register now&#33;
>>> http://p.sf.net/sfu/rsa-sfdev2dev1
>>> _______________________________________________
>>> xmlpipedb-developer mailing list
>>> xml...@li...
>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>> 
>> 
>> ------------------------------------------------------------------------------
>> RSA(R) Conference 2012
>> Save $700 by Nov 18
>> Register now
>> http://p.sf.net/sfu/rsa-sfdev2dev1
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> 
> 
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

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

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

Hi,

Yes, sorry, that is the correct taxon ID and it should be changed.

Best,
Kam

At 04:16 PM 11/2/2011, you wrote:
>Yes, a query for the name should be doable.  It will be a matter of 
>finding the right time/place to do it.
>
>Also, just to confirm, should the taxon ID be changed then to 559292?
>
>John David N. Dionisio, PhD
>Associate Professor, Computer Science
>Associate Director, University Honors Program
>Loyola Marymount University
>
>
>
>On Nov 2, 2011, at 8:41 AM, Kam Dahlquist wrote:
>
> > 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.
> >>>>>
> >>>>>
> >>>>>
> >> 
> ------------------------------------------------------------------------------
> >>>>> All the data continuously generated in your IT infrastructure 
> contains a
> >>>>> definitive record of customers, application performance, security
> >>>>> threats, fraudulent activity and more. Splunk takes this data and makes
> >>>>> sense of it. Business sense. IT sense. Common sense.
> >>>>> http://p.sf.net/sfu/splunk-d2d-oct
> >>>>> _______________________________________________
> >>>>> xmlpipedb-developer mailing list
> >>>>> xml...@li...
> >>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>> <Save_error_1.jpg><Save_error_2.jpg><ATT00001..txt><ATT00002..txt>
> >>
> >>
> >> 
> ------------------------------------------------------------------------------
> >> RSA&#174; Conference 2012
> >> Save $700 by Nov 18
> >> Register now&#33;
> >> http://p.sf.net/sfu/rsa-sfdev2dev1
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> > 
> ------------------------------------------------------------------------------
> > RSA&#174; Conference 2012
> > Save $700 by Nov 18
> > Register now&#33;
> > http://p.sf.net/sfu/rsa-sfdev2dev1
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>------------------------------------------------------------------------------
>RSA(R) Conference 2012
>Save $700 by Nov 18
>Register now
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Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b65 has been released

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

Yes, a query for the name should be doable.  It will be a matter of finding the right time/place to do it.

Also, just to confirm, should the taxon ID be changed then to 559292?

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Nov 2, 2011, at 8:41 AM, Kam Dahlquist wrote:

> 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.
>>>>> 
>>>>> 
>>>>> 
>> ------------------------------------------------------------------------------
>>>>> All the data continuously generated in your IT infrastructure contains a
>>>>> definitive record of customers, application performance, security
>>>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>>>> sense of it. Business sense. IT sense. Common sense.
>>>>> http://p.sf.net/sfu/splunk-d2d-oct
>>>>> _______________________________________________
>>>>> xmlpipedb-developer mailing list
>>>>> xml...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>>> <Save_error_1.jpg><Save_error_2.jpg><ATT00001..txt><ATT00002..txt>
>> 
>> 
>> ------------------------------------------------------------------------------
>> RSA&#174; Conference 2012
>> Save $700 by Nov 18
>> Register now&#33;
>> http://p.sf.net/sfu/rsa-sfdev2dev1
>> _______________________________________________
>> xmlpipedb-developer mailing list
>> xml...@li...
>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> 
> 
> ------------------------------------------------------------------------------
> RSA&#174; Conference 2012
> Save $700 by Nov 18
> Register now&#33;
> http://p.sf.net/sfu/rsa-sfdev2dev1
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

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.
> >>>
> >>>
> >>> 
> ------------------------------------------------------------------------------
> >>> All the data continuously generated in your IT infrastructure contains a
> >>> definitive record of customers, application performance, security
> >>> threats, fraudulent activity and more. Splunk takes this data and makes
> >>> sense of it. Business sense. IT sense. Common sense.
> >>> http://p.sf.net/sfu/splunk-d2d-oct
> >>> _______________________________________________
> >>> xmlpipedb-developer mailing list
> >>> xml...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> > <Save_error_1.jpg><Save_error_2.jpg><ATT00001..txt><ATT00002..txt>
>
>
>------------------------------------------------------------------------------
>RSA&#174; Conference 2012
>Save $700 by Nov 18
>Register now&#33;
>http://p.sf.net/sfu/rsa-sfdev2dev1
>_______________________________________________
>xmlpipedb-developer mailing list
>xml...@li...
>https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

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.
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure contains a
>>> definitive record of customers, application performance, security
>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>> sense of it. Business sense. IT sense. Common sense.
>>> http://p.sf.net/sfu/splunk-d2d-oct
>>> _______________________________________________
>>> xmlpipedb-developer mailing list
>>> xml...@li...
>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> <Save_error_1.jpg><Save_error_2.jpg><ATT00001..txt><ATT00002..txt>

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

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

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.
>>
>>
>>------------------------------------------------------------------------------
>>All the data continuously generated in your IT infrastructure contains a
>>definitive record of customers, application performance, security
>>threats, fraudulent activity and more. Splunk takes this data and makes
>>sense of it. Business sense. IT sense. Common sense.
>>http://p.sf.net/sfu/splunk-d2d-oct
>>_______________________________________________
>>xmlpipedb-developer mailing list
>>xml...@li...
>>https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

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

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

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.
>
>
>------------------------------------------------------------------------------
>All the data continuously generated in your IT infrastructure contains a
>definitive record of customers, application performance, security
>threats, fraudulent activity and more. Splunk takes this data and makes
>sense of it. Business sense. IT sense. Common sense.
>http://p.sf.net/sfu/splunk-d2d-oct
>_______________________________________________
>xmlpipedb-developer mailing list
>xml...@li...
>https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer