> 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? 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. 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. > > 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. > > 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 again for the help, -Amir
