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

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

Just committed the change to the SVN repository; it should no longer try to import lines that begin with an exclamation mark, such as the tag. The release will still not have been effected, only the SVN repository.

Don Murphy




________________________________
From: Don Murphy <djs...@ya...>
To: xml...@li...
Sent: Mon, April 26, 2010 10:18:09 PM
Subject: Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released


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