Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

[Don M. <djs...@ya...>]

I think I see the problem; the method I used for ImportGOAPanel wasn't prepared for the !gaf-version: 2.0 tag at the beginning of the goa file. I was unaware of that being present in the new GAF 2.0 format. I'll work on adapting the export method as soon as possible.

Don Murphy




________________________________
From: "Dahlquist, Kam D." <kda...@lm...>
To: "xml...@li..." <xml...@li...>
Sent: Mon, April 26, 2010 8:48:10 PM
Subject: Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

Hi,

I had to leave for the conference morning while the GO data was processing, so I only did the next step just now.

Here is the report:

UniProt XML import successful.
GO import successful.
GO Processing successful.
GOA import--error.

A screen shot of the error window and the console window (in two parts) is attached.

I was using the source data files that Dondi posted for P. falciparum.

Thanks,
Kam
________________________________________
From: John David N. Dionisio [do...@lm...]
Sent: Sunday, April 25, 2010 9:38 PM
To: xml...@li...
Subject: Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

OK, here's hoping that third time's the charm.  I rebuilt the uniprotdb.jar library in Java 1.5, double-checked that the other XMLPipeDB-authored libraries are also Java 1.5 products, then rebuilt GenMAPP Builder again using Java 1.5.  The 2.0b43 release has been overwritten with this version.

Please redownload and try again; thanks!

John David N. Dionisio, PhD
Assistant Professor, Computer Science
Loyola Marymount University


On Apr 25, 2010, at 7:37 PM, "Dahlquist, Kam D." <kda...@lm...<mailto:kda...@lm...>> wrote:

Hi,

I just downloaded and tried the new build.  It started this time and I configured the database connection, but when I tried to import UniProt XML, I got the attached error, which looks similiar to before.  I tried with both P. falciparum UniProt xml from Dondi and the yeast from Don.

Best,
Kam
________________________________________
From: Don Murphy [djs...@ya...]
Sent: Sunday, April 25, 2010 3:26 PM
To: <mailto:xml...@li...> xml...@li...<mailto:xml...@li...>
Subject: Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

My apologies on the missing source files. I've been using the following sets of source files:

https://www.cs.lmu.edu/biodb/fall2009/index.php/File:MRSA252_2009-11-23.zip for S. aureus
https://www.cs.lmu.edu/biodb/fall2009/index.php/File:Kelia01282010.zip for P. aerugenosa
https://www.cs.lmu.edu/biodb/fall2009/index.php/File:SCbuildresourcesExport3and4.zip for S. cerevisiae

Don Murphy