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. ======================================
