(continuation) Brad Chapman wrote: > > Okay, I'll take an early stand on this issue and go straight for point > number 4, specifically using XDBM as our XML database (side note: did we > come to any conclusions about whether we can safely use this?). We can use it, but we can't package it with Loci. I think we should keep in mind that we may swap it for something more suitable (GPL'd) later on. > My arguments for this: > > 1. I think it will be *a lot* of work to write a database, or map xml into > a relational database like MySQL/PostgreSQL. But I'm not so sure that we even need most of the functionality of a general-purpose database. > 2. I have been looking at XDBM and I really think it does a lot of what we > need (these points are taken from the xdbm documentation) > a. Provides xdbm2xml and xml2xdbm converters. > b. Stores the XML in a pre-parsed format so we don't need to go > through entire XML files to find stuff. > c. You can load only parts of the XML file at a time. > d. Allows you to stored linked lists (the xml:links, I assume) > e. Will support DOM complient interfaces. That all looks very good. > The disadvantages are that XDBM is brand new and probably still has a lot > of bugs to work out. In addition, the "FreeDOM" interfaces which will > supply the DOM complient interface is still under design/development, and > will require a set of python bindings once they are available. The advantages still outweigh the disadvantages. Cheers. Jeff -- +----------------------------------+ | J.W. Bizzaro | | | | http://bioinformatics.org/~jeff/ | | | | THE OPEN LAB | | Open Source Bioinformatics | | | | http://bioinformatics.org/ | +----------------------------------+