On Wed, 2007-09-26 at 14:15 +0200, allank wrote: > Syed Haider wrote: > > >Hi Allan > > > >On Wed, 2007-09-26 at 12:44 +0200, allank wrote: > > > > > >>Hi Syed, > >>As requested, attached please find the configuration files. The filter I > >>am trying to configure has the following characteristics: has an > >>internal name of 'gene_region' and is contained in FilterGroup > >>internalName="hiv_sequence", FilterCollection internalName="hiv_sequence". > >>Looking at the saved xml files, the mid_template.template.xml seems to > >>contain the above data, but the accompanying mid.xml seems to have even > >>a single entry for 'gene_region' filter. > >> > >> > > > >correct, thats one of the known problems, that changes dont propagate > >from template to individual xml. You need to redeclare your filter > >manually as proposed in the last email. > > > > > > > >>Finally, a completely unrelated question, is there a way to load xml > >>documents into marteditor, I remember the older martj did have this option. > >> > >> > > > >If you want to add biomart configuration xmls, yes!, its possible. All > >you need to do is dump the xmls (both .xml and template), followed by > >Upload option of marteditor, then select all the files in one go. > > > > > Thanks Syed, am now interested in manually editing the .xml file for the > shy filters, how do I actually get to upload the xml documents into > marteditor. perhaps, this is dangerous. > For export I would use the File->Export main menu option, what option > (within the file menu? perhaps) may I use for the importation of the same. File->Upload All.
> > > > > > > >>Allan. > >> > >>Syed Haider wrote: > >> > >> > >> > >>>Hi Allan > >>>could you please save your xmls and send them to me, with the name of > >>>the filter causing this trouble. In addition, could you please try > >>>deleting the filter, export. Then, recreate it manually rather copying > >>> > >>> > >>>from another filter, export, check if its displayed. then populate its > >> > >> > >>>option menu, export and see if its displayed. Each time you export, you > >>>need to do perl bin/configure.pl -r conf/your_registry.xml --clean, > >>>kill/restart the server to see the changes on martView. > >>>hope this helps. > >>>cheers > >>>syed > >>> > >>> > >>>On Wed, 2007-09-26 at 11:39 +0200, allank wrote: > >>> > >>> > >>> > >>> > >>>>Hi all, > >>>>I have been having a problem having filters created as lists created in > >>>>marteditor not been displayed in Biomart 0.6. > >>>>Am using Biomart 0.6 and Martj-0.6 (latest release obtained directly > >>>> > >>>> > >>>>from CVS each day I've attempted to solve this puzzle) and PostgreSQL > >>>>8.1.4. > >>> > >>> > >>>>This is how I am creating the filters in a rather conservative way, let > >>>>me explain. In marteditor, I copy a list filter that works (gets > >>>>displayed just fine in Biomart) whose field in the DB is of the same > >>>>type as that of the field on which I am creating the new list based > >>>>filter on, I modify the name and the field name of the copied and now > >>>>pasted control, next I select 'clear option' in it's context menu, then > >>>>after I select 'make drop down' from the context menu. The control get's > >>>>correctly populated with options which are based on unique data values > >>>>of the underlying field and all seems well. I then export the entire > >>>>configuration. I kill biomart process the recommended way, I 'cd' into > >>>>the Biomart perl directory and run 'perl bin/configure.pl --clean -r > >>>>conf/biomart3___postgresql.xml;' command, then I start biomart. Going to > >>>>my webbrower, I click on new on the main menu, I select the dataset and > >>>>so on till I get to select the 'filters' the new filter does not appear. > >>>>What should I do? > >>>> > >>>>Please advise. > >>>> > >>>>Allan. > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >>> > >>> > > > > > >
