Hi, The support for relational databases seems to be tightly coupled to mysql (Please correct me if I'm wrong). In sqlgraph.py for example, database connection defaults to mysql with an explicit import of MySQLdb, search for mysql configuration file variants, etc.
Wouldn't a package like SQLalchemy provide a more transparent way of accessing a relational database backend? This package can handle several database 'engines' and provide a common interface to work with. I'm still a bit unsure whether pygr actually uses the db uri stored in the PYGRDATAPATH environment variable to obtain the connection string. For sure a metabase object is instantiated with the correct 'dbpath', but that object doesn't seem to parse that dbpath parameter. Also, In loading the 'metabases', there is no way to explicitly specify connection parameters (user, host, password, port). I guess I'm still a little confused and I'm learning by placing print statements all over the place... Paul On Tue, Apr 28, 2009 at 12:26 PM, Christopher Lee <l...@chem.ucla.edu>wrote: > > Hi Paul, > can you explain a bit more what you mean by "an extensible on-disk > back-end"? To store what kind of data? Extensible how? > > -- Chris > > > > -- Paul Rigor Graduate Student Institute for Genomics and Bioinformatics Donald Bren School of Information and Computer Sciences University of California in Irvine 248 ICS2 Bldg. +1 (760) 536 - 6767 (skype) --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
