Hi Amir,
On Wed, 2008-02-27 at 09:04 -0500, Amir Karger wrote: > > From: Syed Haider [mailto:[EMAIL PROTECTED] > > > > On Tue, 2008-02-26 at 06:09 -0500, Amir Karger wrote: > > > > > > > while working with MartEditor, you edit template files. These template > > xml files then create individual configs behind the scenes. sometimes, > > changes made in template are not propagated down to the configs. once > > you have loaded martEditor, press Alt+V and you will see the dataset > > configs. you cannot modify these but you can see if they are in sync > > with templates. If they are not, then of course this is a bug which we > > have fixed recently. Again, Richard would be able to provide you with > > the patch. > > Wow. Is Alt+V documented? No, and its not required in normal circumstances. > > More generally, it's not surprising that the docs lag behind the > development, and there is a whole lot of good info in the docs, but it > would be great to have more. > > 1) A table of the fields in martEditor with their allowed options. (The > pictures for displayType are great, by the way. Are those all the > options, though? How does legal_qualifiers work? Etc.) > > 2) A one-page description of what the different steps do: martBuilder > creates the following files; martEditor creates these other files and > also writes this to the DB; configure.pl does.... I think some of this > is already in Getting Started, but consolidating it in one place would > be nice. > > 3) The Getting Started section is nice because it's workflow-driven > (some might say a use case) rather than encyclopedic. Both are > important. But considering that many users will be developing their mart > gradually, a Updating section would be nice. Well, more use cases in > general. "Adding tables", "Adding data to existing tables", or even more > specific examples like "Adding sequence data to position data" (which > just happens to be my goal). That would have relieved my confusion over > what steps need to be taken based on what kind of updating you do. When > do you have to drop a schema, rerun configure, restart apache, etc. you suggestions are valuable and we would improve our docs in due course. > > By the way, it seems to me that many of the martEditor fields have only > a few options. Would you have to revamp the entire code in order to make > most of the fields dropdowns? Seems like it would relieve some > confusion. This is what we are trying to do right now for the release after the next one. A new application will replace MartEditor and would have minimal typing and as you suggested, would have drop downs and options to choose from. > > > > 4. Is there an easy way to reorder options? If I have six > > options, how > > > do I move option 4 to be in between option 2 and 3? > > Anywhere I try to > > > drag, option 4 ends up being placed INSIDE either option 2 or 3. I > > > only managed to reorder by dragging everything in my required order > > > into the container object. > > > > thats possible and if you are unable to achieve this by simple drag n > > drop then its the same problematic bug which we fixed recently. > > I assume this is an as-yet-unbinaried change? I downloaded the 6/27/07 > binary version of marteditor that's still on the FTP site. yes, the new changes to martEditor are not officially released on websites. A little bit of testing to go. > > > > 4a. In the end I may be happier editing the XML file, but I > > don't know > > > where it is right now, and for some changes, it might be nice to use > > > martEditor. > > > > last resort but not recommended, i can guide you through how to edit > > XMLs and where to save them in database using a simple perl > > script. Lets > > first identify the problem and if its as i am expecting, then you will > > be fine by having updated martEditor. > > I love Perl, but for now I'd much prefer to stick with the GUI. Too many > other things to worry about. > > I should mention that overall I think Biomart is great, so I hope my > suggestions are taken as constructive. Thanks a lot. Hope you find the rest of the installation nice and smooth. do write back in case you need further assistance. cheers syed > > Thanks again for the help, > > -Amir -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
