xmlpipedb-developer

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

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

Greetings all,

GenMAPP Builder 2.0b43 has been released.  This release includes the initial version of a major change in how GenMAPP Builder is used: instead of reading the GOA file at export time, it can now be imported into the relational database just like the UniProt and GO XML files.  This change makes exports more streamlined and, based on preliminary testing, speeds up the export process.

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

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

[Bernadette P. <bp...@li...>]

This sounds like such good news.

On Sat, Apr 24, 2010 at 12:12 AM, John David N. Dionisio <do...@lm...>wrote:

> Greetings all,
>
> GenMAPP Builder 2.0b43 has been released.  This release includes the
> initial version of a major change in how GenMAPP Builder is used: instead of
> reading the GOA file at export time, it can now be imported into the
> relational database just like the UniProt and GO XML files.  This change
> makes exports more streamlined and, based on preliminary testing, speeds up
> the export process.
>
> John David N. Dionisio, PhD
> Assistant Professor, Computer Science
> Loyola Marymount University
>
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>

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

[Dahlquist, K. D. <kda...@lm...>]

Hi,

Unfortunately, I cannot run this build.  I get the error "Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file" when I try to run it either from the .bat file or by invoking it from the command line.  I'm attaching a screenshot.

Also, when the new version is up--would you let me know which species and which versions of the source files I should be using for testing?  Please provide me with a  link to the UniProt/GO/GOA files that were used in testing so I can use them myself.

Thanks,
Dr. D
________________________________________
From: John David N. Dionisio [do...@lm...]
Sent: Saturday, April 24, 2010 12:12 AM
To: xml...@li...
Subject: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

Greetings all,

GenMAPP Builder 2.0b43 has been released.  This release includes the initial version of a major change in how GenMAPP Builder is used: instead of reading the GOA file at export time, it can now be imported into the relational database just like the UniProt and GO XML files.  This change makes exports more streamlined and, based on preliminary testing, speeds up the export process.

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



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xml...@li...
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Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

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

Greetings,

Oh, so sorry...I could have sworn I flipped the "Java 1.5" switch.  Since it's pretty much identical, I just overwrote the current file on SourceForge with a Java 1.5-compatible version.  A re-download at this point should get you that version.

I did not find any student links (particularly from Don) to any test files.  In principle, however, this version should work with any current-format files, so I just downloaded a fresh set of P. falciparum for starters.  I zipped the UniProt, GO, and OBO-XML files and uploaded the file to the biodb2009 wiki:

	https://www.cs.lmu.edu/biodb/fall2009/images/0/0a/Goa-database-test-20100425.zip

In case the direct link doesn't work, there is also a link to it on my biodb2009 user page:

	https://www.cs.lmu.edu/biodb/fall2009/index.php/User:Dondi

If this first test goes well, we can download additional species, culminating perhaps in yeast.

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


On Apr 25, 2010, at 10:34 AM, Dahlquist, Kam D. wrote:

> Hi,
> 
> Unfortunately, I cannot run this build.  I get the error "Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file" when I try to run it either from the .bat file or by invoking it from the command line.  I'm attaching a screenshot.
> 
> Also, when the new version is up--would you let me know which species and which versions of the source files I should be using for testing?  Please provide me with a  link to the UniProt/GO/GOA files that were used in testing so I can use them myself.
> 
> Thanks,
> Dr. D

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

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

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



________________________________
From: John David N. Dionisio <do...@lm...>
To: "xml...@li..." <xml...@li...>
Sent: Sun, April 25, 2010 1:51:29 PM
Subject: Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

Greetings,

Oh, so sorry...I could have sworn I flipped the "Java 1.5" switch.  Since it's pretty much identical, I just overwrote the current file on SourceForge with a Java 1.5-compatible version.  A re-download at this point should get you that version.

I did not find any student links (particularly from Don) to any test files.  In principle, however, this version should work with any current-format files, so I just downloaded a fresh set of P. falciparum for starters.  I zipped the UniProt, GO, and OBO-XML files and uploaded the file to the biodb2009 wiki:

    https://www.cs.lmu.edu/biodb/fall2009/images/0/0a/Goa-database-test-20100425.zip

In case the direct link doesn't work, there is also a link to it on my biodb2009 user page:

    https://www.cs.lmu.edu/biodb/fall2009/index.php/User:Dondi

If this first test goes well, we can download additional species, culminating perhaps in yeast.

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


On Apr 25, 2010, at 10:34 AM, Dahlquist, Kam D. wrote:

> Hi,
> 
> Unfortunately, I cannot run this build.  I get the error "Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file" when I try to run it either from the .bat file or by invoking it from the command line.  I'm attaching a screenshot.
> 
> Also, when the new version is up--would you let me know which species and which versions of the source files I should be using for testing?  Please provide me with a  link to the UniProt/GO/GOA files that were used in testing so I can use them myself.
> 
> Thanks,
> Dr. D


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xml...@li...
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Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

[Dahlquist, K. D. <kda...@lm...>]

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: 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

________________________________
From: John David N. Dionisio <do...@lm...>
To: "xml...@li..." <xml...@li...>
Sent: Sun, April 25, 2010 1:51:29 PM
Subject: Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released

Greetings,

Oh, so sorry...I could have sworn I flipped the "Java 1.5" switch.  Since it's pretty much identical, I just overwrote the current file on SourceForge with a Java 1.5-compatible version.  A re-download at this point should get you that version.

I did not find any student links (particularly from Don) to any test files.  In principle, however, this version should work with any current-format files, so I just downloaded a fresh set of P. falciparum for starters.  I zipped the UniProt, GO, and OBO-XML files and uploaded the file to the biodb2009 wiki:

    https://www.cs.lmu.edu/biodb/fall2009/images/0/0a/Goa-database-test-20100425.zip

In case the direct link doesn't work, there is also a link to it on my biodb2009 user page:

    https://www.cs.lmu.edu/biodb/fall2009/index.php/User:Dondi

If this first test goes well, we can download additional species, culminating perhaps in yeast.

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


On Apr 25, 2010, at 10:34 AM, Dahlquist, Kam D. wrote:

> Hi,
>
> Unfortunately, I cannot run this build.  I get the error "Exception in thread "main" java.lang.UnsupportedClassVersionError: Bad version number in .class file" when I try to run it either from the .bat file or by invoking it from the command line.  I'm attaching a screenshot.
>
> Also, when the new version is up--would you let me know which species and which versions of the source files I should be using for testing?  Please provide me with a  link to the UniProt/GO/GOA files that were used in testing so I can use them myself.
>
> Thanks,
> Dr. D


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xmlpipedb-developer mailing list
xml...@li...<mailto%3A%25e%25>
https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer

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

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

Ack, sorry, that's the updated UniProt database library complaining now.  That codebase was built when the UniProt XSD was modified...for that one, I realize now, I was not even thinking about the 1.5/1.6 version distinction.  I guess the students tested that on 1.6 systems, thus explaining why this issue has not been caught until now.

I'll rebuild from bottom up in 1.5 then send another message when it's online. 

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...> 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: 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

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

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

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...> 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: 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

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

[Bernadette P. <bp...@li...>]

I will try.

On 4/25/10, John David N. Dionisio <do...@lm...> wrote:
>
>  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...>
> 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: 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.zipfor 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.zipfor S. cerevisiae
>
> Don Murphy
>
>
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>

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

[Dahlquist, K. D. <kda...@lm...>]

Hi,

This one is working--will let you know when I have gdb finished.

Best,
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

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

[Dahlquist, K. D. <kda...@lm...>]

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

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