DbObj is context-specific - for a certain network xml adaptor I am writing, it is called Session. I like making a separation between Context and adaptor. Context is the module that organizes the various adaptors - it calls them all and assigns them to their objects. So I thought of Context being the parent, and the adaptors being Context's children. Oh, I see your confusion. You are putting the stuff in at the wrong level. You need to create a new folder called GB at the same level as DAS and DB. Then your Context implementation becomes GQ::Server::GB::Context, and your adaptors become "GQ::Server::GB::Adaptor::XYZAdaptor"s. The tricky part in the adaptor layer is loading stuff from the data source and storing it. The editing part almost writes itself - you just have to change update_db and you're done. I would cd DB/Adaptor; grep prepare * | lpr and make sure all of the database calls are taken care of in your adaptors. Have fun! Dave On Tuesday, December 18, 2001, at 07:26 AM, Mark Wilkinson wrote: > Hey Dave! > > I have decided (since we are about to publish the Genquire paper and > book > chapter) that it is about time we tested this adaptor API to ensure that > a person with half a brain can put together their own adaptor layer... > and I seem like a perfect candidate for THAT job!! ;-) > > I have imediately hit a point of confusion: > > In the gq_local.cfg file the first thing that is created is a DbObj, and > this is sent as an initialization parameter for Context. Is it > necessary > for all Adaptor layers to have a DbObj, or is this required only by our > own Genquire_local adaptor? If the latter, then I will add a note in > the > gq_local.cfg file indicating this, and will also clarify the API docs. > It seems to be that the only thing that calls DbObj is the Context > module > itself, so I am guessing that a DbObj is not a 'deep' part of Genquire. > > I am also wondering if it might be a good idea to put Context.pm into > the > /Adaptor/ folder, since any new adaptor is going to require its own > version of the Context module anyway (according to the API docs). I am > guessing we can leave ContextI where it is, since it should be common to > all adaptors, but Context.pm itself seems to belong with its > "brothers".... what say you? > > To make my own adaptor layer, I have created a new folder > /GB_FlatAdaptor/ and copied all of the modules from /Adaptor? into that > folder. I then updated the identities of the package statements, and > the > @ISA and use statements. There isn't anything more to this... right?... > no hidden land mines that I should look out for? (at least, none that > you know about...) > > To be honest, it looks like it is going to be quite straightforward. My > gb_flat.cfg file is going to create a BioPerl Seq object from the GB > flat > file, so I already have almost all of the Genquire functionality right > at > hand before I even start coding!! > > please get back to me with *quick* answers ASAP so that I can continue. > > Actually, this looks like it is going to be a lot of fun!!! I like > being > a guinea pig 8^) > > M > > > > -- > -------------------------------- > "Speed is subsittute fo accurancy." > ________________________________ > > Dr. Mark Wilkinson > Bioinformatics Group > National Research Council of Canada > Plant Biotechnology Institute > 110 Gymnasium Place > Saskatoon, SK > Canada > > > > > > _______________________________________________ > Genquire-dev maillist - Genquire-dev@bioinformatics.org > http://bioinformatics.org/mailman/listinfo/genquire-dev > > David Block (858)812-1513 Bioinformatics http://www.gnf.org dblock@gnf.org Just ridin' the Coaster...