Hi Andrew this seems to be very specific to your environment, as the same distro on my XP works for same xml's while it refuse to on your side. could you do a simple database, say one main table and one or two entries in it, then run naive and export from MEditor, and see if it fails.
many thanks for your patience. syed On Thu, 2007-09-20 at 15:00 -0500, Vallejos, Andrew wrote: > I have write access. I can import and export configurations. > > -----Original Message----- > From: Syed Haider [mailto:[EMAIL PROTECTED] > Sent: Thursday, September 13, 2007 11:25 AM > To: Vallejos, Andrew > Cc: mart-dev > Subject: RE: [mart-dev] Duplicate Entry Error > > On Thu, 2007-09-13 at 16:27 +0100, Syed Haider wrote: > > Hi Andrew > > > > just tested your xmls, using MartEditor from (.zip) distro available > on > > our website DOCS > > > > > ftp://[EMAIL PROTECTED]/pub/software/biomart/martj_current/martj-b > in.zip > > > > > > it works fine and creates datasets correctly. > > forgot to mention :) i tested this on WIN XP > > > However the ERROR: "File does not contain valid configuration" is > thrown > > when the connection to database doesnt support write access. > > could you please double check this and also try using the distro's > > martj-bin.zip if you are using a locally compiled batch file. > > > > may be this would give us some pointers. > > > > thanks > > syed > > > > > > On Wed, 2007-09-12 at 09:49 -0500, Vallejos, Andrew wrote: > > > Still doesn't work. > > > > > > I am using the mart-j tools for windows (not sure if that makes a > > > difference). > > > > > > -Andrew > > > > > > -----Original Message----- > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > Sent: Wednesday, September 12, 2007 9:45 AM > > > To: Vallejos, Andrew > > > Cc: mart-dev > > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > > > Hi Andrew > > > > > > attached are the two files you sent to me yesterday. > > > Just now, I have created a new database, using marteditor 0.6, I > > > connected to this new database, uploaded ('Upload All') the files by > > > selecting both simultaneously, then did 'import' and it works fine. > > > > > > could you please see if these two help you recover your work. > > > > > > cheers > > > syed > > > > > > > > > On Wed, 2007-09-12 at 09:15 -0500, Vallejos, Andrew wrote: > > > > I deleted it using the martEditor. > > > > > > > > I've tried loading both the single file and loading both the > regular > > > > file and the *.template file together. > > > > > > > > -Andrew > > > > > > > > -----Original Message----- > > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > Sent: Wednesday, September 12, 2007 9:11 AM > > > > To: Vallejos, Andrew > > > > Cc: mart-dev > > > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > > > > > to further diagnose this: > > > > - did you delete it using martEditor or you tried manual deletion > from > > > > files ? > > > > > > > > - secondarily when you try to load xml from MartEditor, you need > to > > > load > > > > *template.xml file, are you loading this one ? > > > > > > > > > > > > On Wed, 2007-09-12 at 09:06 -0500, Vallejos, Andrew wrote: > > > > > > > If so, then i would suggest to delete the existing filter > which > > > is > > > > > > > causing you the trouble and redeclare it. hopefully that > will > > > work > > > > > > > out. > > > > > > > > > > I deleted the existing filter list per your suggestion, and to > save > > > > time > > > > > I saved a copy of the original xml and was going to load the > saved > > > > copy > > > > > rather than recreate the filter list. > > > > > > > > > > -Andrew > > > > > > > > > > -----Original Message----- > > > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > > Sent: Wednesday, September 12, 2007 9:04 AM > > > > > To: Vallejos, Andrew > > > > > Cc: mart-dev > > > > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > > > > > > > Hi Andrew > > > > > > > > > > On Wed, 2007-09-12 at 08:57 -0500, Vallejos, Andrew wrote: > > > > > > I cannot load my saved xml file(s). > > > > > > > > > > > > I get an error from the marteditor. > > > > > > > > > > > > "File does not contain valid configuration." > > > > > > > > > > thats not encouraging....this might be a problem with > MartEditor. > > > > > Is there a chance that you do not need to reload your xmls and > you > > > > just > > > > > connect to your database and do import. why do you have to use > saved > > > > > xmls ? > > > > > > > > > > > > > > > > > > > > > > -Andrew > > > > > > > > > > > > -----Original Message----- > > > > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > > > Sent: Wednesday, September 12, 2007 8:47 AM > > > > > > To: Vallejos, Andrew > > > > > > Cc: mart-dev > > > > > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > > > > > > > > > > > > > > > > > > > > > On Wed, 2007-09-12 at 08:43 -0500, Vallejos, Andrew wrote: > > > > > > > perl bin/configure.pl --clean -r con/your_registry.xml > --clean > > > > > > > > > > > > > > is the exact syntax that I use. Does it matter than the > > > '--clean' > > > > > is > > > > > > in > > > > > > > a different location? > > > > > > > > > > > > no, as long as its there, its fine. > > > > > > did you try removing existing filter and adding a new one ? > > > > > > > > > > > > cheers > > > > > > syed > > > > > > > > > > > > > > > > > > > > -Andrew > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > > > > Sent: Wednesday, September 12, 2007 4:57 AM > > > > > > > To: Vallejos, Andrew; mart-dev > > > > > > > Subject: RE: [mart-dev] Duplicate Entry Error > > > > > > > > > > > > > > Hi Andrew > > > > > > > Could you please confirm if once doing the 'export' from > > > > MartEditor, > > > > > > you > > > > > > > do reconfigure BioMart > > > > > > > > > > > > > > perl bin/configure.pl -r con/your_registry.xml --clean > > > > > > > > > > > > > > and kill/restart your server ? > > > > > > > > > > > > > > If so, then i would suggest to delete the existing filter > which > > > is > > > > > > > causing you the trouble and redeclare it. hopefully that > will > > > work > > > > > > out. > > > > > > > > > > > > > > cheers > > > > > > > syed > > > > > > > > > > > > > > > > > > > > > On Tue, 2007-09-11 at 13:52 -0500, Vallejos, Andrew wrote: > > > > > > > > Syed, > > > > > > > > > > > > > > > > Ok, so I am not getting the duplication error anymore. > > > However, > > > > I > > > > > > > have > > > > > > > > filters that are not showing up. > > > > > > > > > > > > > > > > The chromosome filter for gene map v3.4 and the disease > > > ontology > > > > > > > filters > > > > > > > > are not displaying on martview page. The chromosome I did > get > > > > to > > > > > > > > display once, but then it disappeared the next time I > updated > > > > the > > > > > > > file. > > > > > > > > > > > > > > > > -Andrew > > > > > > > > > > > > > > > > -----Original Message----- > > > > > > > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > > > > > Sent: Friday, September 07, 2007 3:34 AM > > > > > > > > To: Vallejos, Andrew > > > > > > > > Cc: [email protected] > > > > > > > > Subject: Re: [mart-dev] Duplicate Entry Error > > > > > > > > > > > > > > > > Hi Andrew > > > > > > > > > > > > > > > > On Thu, 2007-09-06 at 15:44 -0500, Vallejos, Andrew wrote: > > > > > > > > > We've recently installed a test v0.6 mart. However, now > > > that > > > > I > > > > > am > > > > > > > > > using the v0.6 tools I keep receiving a "Remove > Duplicates > > > > > before > > > > > > > > > generating Template" error. > > > > > > > > > > > > > > > > is it martEditor which throws this error ? If so, please > send > > > me > > > > > > your > > > > > > > > xmls. I assume you get this error when you 'export'. > Please > > > > > correct > > > > > > me > > > > > > > > if thats not the case. > > > > > > > > > > > > > > > > thanks > > > > > > > > syed > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I have no idea why I am getting this error as I have no > > > > > duplicates > > > > > > > in > > > > > > > > > my attribute tables, I've checked. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -Andrew > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ====================== > > > > > > > > > > > > > > > > > > Andrew Vallejos > > > > > > > > > > > > > > > > > > Web Developer > > > > > > > > > > > > > > > > > > Medical College of Wisconsin > > > > > > > > > > > > > > > > > > 414-955-4104 > > > > > > > > > > > > > > > > > > [EMAIL PROTECTED] > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > ====================================== > > > > > Syed Haider. > > > > > EMBL-European Bioinformatics Institute > > > > > Wellcome Trust Genome Campus, Hinxton, > > > > > Cambridge CB10 1SD, UK. > > > > > ====================================== > > > > > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
