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From: Kam D. <kda...@lm...> - 2010-08-23 22:49:06
|
Hi, Sounds good. I tried the vista.bat, but it won't open the program, so I'll wait for the update on Windows 7. In the meantime, I can still test on XP. The progress bar thing was more of a "I don't know how this is supposed to look" type thing. I've just never seen a behavior like that before. I think it's fine--it conveys that something is happening to the user and that he/she should wait. Cheers, Kam At 12:02 PM 8/23/2010, John David N. Dionisio wrote: >Greetings, > >The Access database location issue is probably the same one >encountered with Vista. We had some code in there that goes >something like "if it's Vista, look for the Jet engine >here..." We'll probably need an equivalent for Windows 7; I'll look it up. > >The progress bar look is, unfortunately, Java's standard look for >progress bars that don't display definite amounts done. The display >of definite values may or may not be possible, depending on whether >a mechanism exists for reporting how much progress has been made >(many of our import calls are "one-liners" --- i.e., one invokes the >command and waits for it to be done; there is no default "status >report" as the command is in progress). I can look into that, but >there is a chance that it may not be possible (especially for the >code that relies on other libraries in particular). > >John David N. Dionisio, PhD >Associate Professor, Computer ScienceHi, >Loyola Marymount University > > > >On Aug 22, 2010, at 8:59 PM, Kam Dahlquist wrote: > > > Hi, > > > > Good news and bad news. gmb2b50 works on XP--I didn't put it through > > all of its paces, but it imports and exports Vibrio OK. However, it > > has a couple issues on my new Windows 7 setup. > > > > 1. When I go through the export wizard, it doesn't see all of the > > database xrefs, so it only asks me about the OrderedLocus and > > GeneOntology tables. (it does see them in XP) > > > > 2. The export crashes with the error attached. It seems to have > > something to do with connecting to the Access database--you would > > know better, but I'm guessing that there were changes made to the > > Microsoft Jet engine in 7? > > > > Not an exclusive 7 issue, I'm not sure how the progress bar you used > > should behave, but what it looks like is pong, the bar slides back > > and forth in the window, it doesn't show progress, per se, just more > > like an indicator that it is busy. > > > > I'll go back to testing on XP for the time being so that I can look > > at all the changes made. > > > > Cheers, > > Kam > > >------------------------------------------------------------------------------ >Sell apps to millions through the Intel(R) Atom(Tm) Developer Program >Be part of this innovative community and reach millions of netbook users >worldwide. Take advantage of special opportunities to increase revenue and >speed time-to-market. Join now, and jumpstart your future. >http://p.sf.net/sfu/intel-atom-d2d >_______________________________________________ >xmlpipedb-developer mailing list >xml...@li... >https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
From: John D. N. D. <do...@lm...> - 2010-08-23 19:03:05
|
Greetings, The Access database location issue is probably the same one encountered with Vista. We had some code in there that goes something like "if it's Vista, look for the Jet engine here..." We'll probably need an equivalent for Windows 7; I'll look it up. The progress bar look is, unfortunately, Java's standard look for progress bars that don't display definite amounts done. The display of definite values may or may not be possible, depending on whether a mechanism exists for reporting how much progress has been made (many of our import calls are "one-liners" --- i.e., one invokes the command and waits for it to be done; there is no default "status report" as the command is in progress). I can look into that, but there is a chance that it may not be possible (especially for the code that relies on other libraries in particular). John David N. Dionisio, PhD Associate Professor, Computer Science Loyola Marymount University On Aug 22, 2010, at 8:59 PM, Kam Dahlquist wrote: > Hi, > > Good news and bad news. gmb2b50 works on XP--I didn't put it through > all of its paces, but it imports and exports Vibrio OK. However, it > has a couple issues on my new Windows 7 setup. > > 1. When I go through the export wizard, it doesn't see all of the > database xrefs, so it only asks me about the OrderedLocus and > GeneOntology tables. (it does see them in XP) > > 2. The export crashes with the error attached. It seems to have > something to do with connecting to the Access database--you would > know better, but I'm guessing that there were changes made to the > Microsoft Jet engine in 7? > > Not an exclusive 7 issue, I'm not sure how the progress bar you used > should behave, but what it looks like is pong, the bar slides back > and forth in the window, it doesn't show progress, per se, just more > like an indicator that it is busy. > > I'll go back to testing on XP for the time being so that I can look > at all the changes made. > > Cheers, > Kam |
From: Kam D. <kda...@lm...> - 2010-08-23 18:33:22
|
Hi, Good news and bad news. gmb2b50 works on XP--I didn't put it through all of its paces, but it imports and exports Vibrio OK. However, it has a couple issues on my new Windows 7 setup. 1. When I go through the export wizard, it doesn't see all of the database xrefs, so it only asks me about the OrderedLocus and GeneOntology tables. (it does see them in XP) 2. The export crashes with the error attached. It seems to have something to do with connecting to the Access database--you would know better, but I'm guessing that there were changes made to the Microsoft Jet engine in 7? Not an exclusive 7 issue, I'm not sure how the progress bar you used should behave, but what it looks like is pong, the bar slides back and forth in the window, it doesn't show progress, per se, just more like an indicator that it is busy. I'll go back to testing on XP for the time being so that I can look at all the changes made. Cheers, Kam |
From: Dahlquist, K. D. <kda...@lm...> - 2010-05-03 20:37:26
|
Hi, Just wanted to let everyone know that the Staphyloccus aureus gdb checks out with the gmb2b44 release. So, Don's code has been vetted for S. aureurs, V. cholerae, P. falciparum, and S. cerevisiae. Best, Dr. D |
From: John D. N.D. <do...@lm...> - 2010-04-30 18:29:36
|
OK, good to hear that things work. Sorry about that beta label...I forgot to update on the last quick-turnaround update. I'll tweak it and let you know when it's there. John David N. Dionisio, PhD Assistant Professor, Computer Science Loyola Marymount University On Apr 30, 2010, at 10:35 AM, Dahlquist, Kam D. wrote: > Hi, > > The Vibrio export run with 2.0b44 checks out. It is identical to the one we ran a few weeks ago with the same data. I think we can be confident that the changes Don made are working--they have been tested with Vibrio, Plasmodium, and yeast. > > One little thing--the title bar of GenMAPP Builder for b44 still refers to b43 and thus, this is what gets filled into the notes field. Not a big deal in terms of function, but it makes keeping track of versions a little more difficult. > > Best, > Dr. D > ------------------------------------------------------------------------------ > _______________________________________________ > xmlpipedb-developer mailing list > xml...@li... > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-30 17:38:49
|
Hi, The Vibrio export run with 2.0b44 checks out. It is identical to the one we ran a few weeks ago with the same data. I think we can be confident that the changes Don made are working--they have been tested with Vibrio, Plasmodium, and yeast. One little thing--the title bar of GenMAPP Builder for b44 still refers to b43 and thus, this is what gets filled into the notes field. Not a big deal in terms of function, but it makes keeping track of versions a little more difficult. Best, Dr. D |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-27 17:50:53
|
Hi, The plasmodium gdb exported successfully. The TallyEngine reports concordance between the IDs in XML and Postgres--there seems to be a few missing IDs for GeneId and RefSeq in the gdb, but it does color a MAPP correctly, so the discrepancy is probably not due to the GOA processing. I will run an export on another species tonight--probably vibrio. Cheers, Kam ________________________________________ From: John David N. Dionisio [do...@lm...] Sent: Tuesday, April 27, 2010 1:11 AM To: xml...@li... Subject: Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released OK, I've released Don's update as GenMAPP Builder 2.0b44. Rinse and repeat... John David N. Dionisio, PhD Assistant Professor, Computer Science Loyola Marymount University On Apr 26, 2010, at 10:55 PM, Don Murphy wrote: > 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 > ------------------------------------------------------------------------------ _______________________________________________ xmlpipedb-developer mailing list xml...@li... https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-27 14:42:17
|
Hi, I imported the GOA into the Postgres database I had already started with gmb2b43. I'm now running an export--will let you know the results when I get out of class. Best, Kam ________________________________________ From: John David N. Dionisio [do...@lm...] Sent: Tuesday, April 27, 2010 1:11 AM To: xml...@li... Subject: Re: [XMLPipeDB-developer] GenMAPP Builder 2.0b43 has been released OK, I've released Don's update as GenMAPP Builder 2.0b44. Rinse and repeat... John David N. Dionisio, PhD Assistant Professor, Computer Science Loyola Marymount University On Apr 26, 2010, at 10:55 PM, Don Murphy wrote: > 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 > ------------------------------------------------------------------------------ _______________________________________________ xmlpipedb-developer mailing list xml...@li... https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
From: John D. N. D. <do...@lm...> - 2010-04-27 08:11:19
|
OK, I've released Don's update as GenMAPP Builder 2.0b44. Rinse and repeat... John David N. Dionisio, PhD Assistant Professor, Computer Science Loyola Marymount University On Apr 26, 2010, at 10:55 PM, Don Murphy wrote: > 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 M. <djs...@ya...> - 2010-04-27 05:56:02
|
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 |
From: Don M. <djs...@ya...> - 2010-04-27 05:18:19
|
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 |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-27 03:50:55
|
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 |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-26 16:32:36
|
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 |
From: Bernadette P. <bp...@li...> - 2010-04-26 05:26:36
|
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 > > |
From: John D. N. D. <do...@lm...> - 2010-04-26 04:38:22
|
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 |
From: John D. N. D. <do...@lm...> - 2010-04-26 03:31:06
|
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 |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-26 02:39:41
|
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 ------------------------------------------------------------------------------ _______________________________________________ xmlpipedb-developer mailing list xml...@li...<mailto%3A%25e%25> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
From: Don M. <djs...@ya...> - 2010-04-25 22:26:22
|
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 ------------------------------------------------------------------------------ _______________________________________________ xmlpipedb-developer mailing list xml...@li... https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
From: John D. N. D. <do...@lm...> - 2010-04-25 20:51:40
|
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 |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-25 17:38:10
|
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 ------------------------------------------------------------------------------ _______________________________________________ xmlpipedb-developer mailing list xml...@li... https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer |
From: Bernadette P. <bp...@li...> - 2010-04-24 08:16:11
|
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 > |
From: John D. N. D. <do...@lm...> - 2010-04-24 07:12:34
|
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 |
From: John D. N. D. <do...@lm...> - 2010-04-15 07:07:49
|
The XMLPipeDB project has released standard Pseudomonas aeruginosa str. PAO1 and Staphylococcus aureus (strain MRSA252) Gene Databases. Detailed information on these databases is contained in the included ReadMes. John David N. Dionisio, PhD Assistant Professor, Computer Science Loyola Marymount University |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-15 04:58:57
|
Hi, I've finished editing the ReadMe and giving the visual inspection for the Pseudomonas database. I've put the release versions of the ReadMe and the zipped Readme and gdb on Kelia's BioDB page here: https://www.cs.lmu.edu/biodb/fall2009/index.php/Kmspring2010#Release_Version_Pseudomonas_aerugenosa So, as soon as you have a chance, it would be great if you could release it on the SourceForge site. Best, Kam |
From: Dahlquist, K. D. <kda...@lm...> - 2010-04-15 02:37:14
|
Hi, I've finished editing the ReadMe and giving the visual inspection for the Staph aureus database. I've put the release versions of the ReadMe and the zipped Readme and gdb on Kelly's BioDB page here: https://www.cs.lmu.edu/biodb/fall2009/index.php/Kparks3research2010#Release_Versions So, as soon as you have a chance, it would be great if you could release it on the SourceForge site. Best, Kam |