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Re: [Gusdev-gusdev] DoTS:NAEntry and topology
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From: Angel P. <an...@pc...> - 2004-01-21 17:56:07
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BTW, I did not mention this, but adding a column in the GUS system is not completely trivial. Since the default columns are assumed to be at the end of the column list, and adding a column in most RDBMSs appends to the column list, you in fact have to create a new temporary table where the added column precedes the "modification_date". The added column is usually nullable and thus a select statement is used to populate the temp table from the old: insert into <new_table> (<column list from old table>) select * from <original_table>; If the column is to be non-null, then you have to provide some default value in the column listing of the select clause of the insert statement: insert into <new_table> (<column list from NEW table>) select <non default columns from old table>, <default_value>, <GUS default column list> from <original_table>; Then you rename the old/new tables, drop and recreate the constraints (the constraints will follow the old table as you rename, so if you don't drop them first or you will have name clashes) and then the object layer sees the new table definition. I'll release this as GUS 3.1.1 Angel Angel Pizarro wrote: > Adding the column will not break anythiing, although I ask you to post > a tracker item on the SF.net site. : > > http://sourceforge.net/tracker/?atid=479181&group_id=54213&func=browse > > Also, please attach the SQL to make that makes the new table, > transfers the data, apply constraints and rename the tables > appropriately, etc., to the tracker item. Since you have to do these > actions regardless, it would be nice to share them as a script ;) > > I'll commit the change to CVS when I make the other changes that are > needed for GUS 3.1 > > Angel > > Fidel Salas wrote: > >> Chris Stoeckert <sto...@pc...> writes: >> >> > Hi Fidel, >> >> Hi Chris. Thanks for your response. >> >> > What are you trying to get from LOCUS? >> > Here's an example for the kit gene (maybe you can send me a more >> > relevant one for you). >> > LOCUS NM_021099 5132 bp mRNA linear ROD 20-DEC-2003 >> > Is it the "linear" info? >> >> Yes, it is the "linear" (or "circular") info. >> >> > I agree that NAEntry table would be a good place for this and I >> would >> > recommend that the NAEntry table have a "topology" attribute >> added. >> > I'm guessing that this information was lost because it's not >> something >> > that we at CBIL use. >> >> Understood. >> >> > My understanding is that nothing should should break by adding >> this >> > column but would like others to confirm (Steve? Angel?) >> >> It sounds good. >> >> Fidel >> >> >> > I also don't think that you would need to add set/get methods just >> > alter the existing one for NAEntry. >> >> >> > Chris >> >> >> > On Jan 6, 2004, at 11:35 AM, Fidel Salas wrote: >> >> >> > I need help in finding a quick solution to the following >> requirement. >> >> >> > I need topology information for any given GenBank DNA sequence or >> > entry. This information is found in the LOCUS line of a GenBank >> > entry. For reasons unclear to me, the GBParser plugin parses >> this and >> > then silently drops it. >> >> >> > Since I am about to create a new GUS database, I would like to >> add a >> > column to DoTS:NAEntry that will hold the topology >> information. The >> > main question is: will I break anything if I add this column to >> the >> > tables sql script? >> >> >> > Also, what is the reason this information is dropped? >> >> >> > I am assuming getting GBParser to populate this new column would >> > involve just getting the objrelp generator to add set and get >> methods. >> > Is this all that would need to be done? >> >> >> > Thanks >> >> >> > Fidel >> >> >>> >>> >>> >> >> > ------------------------------------------------------- >> > This SF.net email is sponsored by: IBM Linux Tutorials. >> > Become an expert in LINUX or just sharpen your skills. Sign up >> for >> > IBM's >> > Free Linux Tutorials. Learn everything from the bash shell to sys >> > admin. >> > Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click >> > _______________________________________________ >> > Gusdev-gusdev mailing list >> > Gus...@li... >> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> ------------------------------------------------------- >> The SF.Net email is sponsored by EclipseCon 2004 >> Premiere Conference on Open Tools Development and Integration >> See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. >> http://www.eclipsecon.org/osdn >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > > > > ------------------------------------------------------- > The SF.Net email is sponsored by EclipseCon 2004 > Premiere Conference on Open Tools Development and Integration > See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. > http://www.eclipsecon.org/osdn > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
