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Re: [Gusdev-gusdev] GBParser
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From: MICHAEL L. <lu...@cs...> - 2004-05-21 14:22:26
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Hey Jinal- It is kind of important to know what's going on with the algorithm_id. Almost every table in GUS has a field called row_alg_invocation_id that is a primary foriegn key. I will attempt to explain, and maybe someone can clarify my lack of knowledge. But this is strongly tied to the whole ga/plugin structure. Every plugin that you use is an an algorithm. When you use ga +create SomePlugin it puts an entry into the algorithm table for that plug-in, and I assume an initial entry into the algorithmImplementation table. When you do a ga +update SomePlugin it puts a new entry into into the algorithmImplementation table with the same algorithm_id. This way you can keep updating your plug-ins from CVS. So, depending on how many times you run ga +update SomePlugin, you can have that many rows in algorithmImplementation with the algorithm_id that corresponds to SomePlugin. Once that's in there, every time you <i>use</i> SomePlugin, ga places an entry into algorithmInvocation, with a new algorithm_invocation_id , and an algorithm_implentation_id corresponding to the version of the plugin you are running. This is usefull for when you have entered a bunch of data using SomePlugin, and then you find out that SomePlugin had a bug in it and you placed the data in an incorrect place, or entered incorrect data. You can then remove everything that has the row_alg_invocation_id equal to the algorithm_invocation_id that messed up. Now, this collection of tables is really circular, with algorithmInvocation having a self-referential primary key, but I think that the install of GUS will take care of it. I assume that ga itself is an algorithm. My oracle is down right now so I can't check. I couldn't answer your question directly before because I distinctly remember entering a row in Algorithm once for an annotation ID, so if I don't know the particulars of the plugin, can't say for sure what you need. But I might remember distinctly doing something wrong, since I was still quite the nube back then(now I am only a little less wet-behind-the-ears). I don't know if every algorithm is a plugin, and every plugin is an algorithm(ie a one-to-one correspondence), or if every plug-in is an algorithm but not every algorithm is a plugin-- you know like all shriners are masons but not all masons are shriners. If anyone wants to clarify this, feel free. Michael Luchtan http://www.cs.uga.edu/~luchtan On Thu, 20 May 2004, jinal jhaveri wrote: > I am using CVS Version 1.30 > > ----- Original Message ----- > From: MICHAEL LUCHTAN <lu...@cs...> > Date: Thursday, May 20, 2004 6:21 am > Subject: Re: [Gusdev-gusdev] GBParser > > > Actually I answered the second question. But I was willing to give a try > > at the third. But upon looking at my GBParser module, there IS NO > > arguement for algoinvo. I have CVS version 1.17. Jinal, what are you > > running? Unfortunately, I can't remember if we modified these here or > > not, but I don't think that we did. Here is our module, attached. > > > > > > Michael Luchtan > > http://www.cs.uga.edu/~luchtan > > > > > > On Thu, 20 May 2004, Steve Fischer wrote: > > > > > jinal- > > > > > > see below > > > > > > jinal jhaveri wrote: > > > > > > >Hi, > > > > > > > >I have some questions regarding the GBParser module > > > > > > > >1) First required field is --gbRel. As I understand this is genbank's > > db realease id. Now where do I get this number from? ( genbanks > > website????) Does anybody has idea about what is the release right now on web? > > > > > > > > > > > yes, this is from the readme file . it is stored in GUS in the > > > created_rel_ver and updated_rel_ver attributes of the DoTS::NAEntry table: > > > http://www.gusdb.org/cgi- > > bin/schemaBrowser?db=CBILBLD&table=DoTS::NAEntry&path=DoTS::NAEntry> > > > >2) --db_rel_id : As the documentation describes, this is external > > database id. Do I create this id on my own? Do I need to keep this entry > > in any other table? Does this id has one to one correspondence with the > > project I am working on (and the one I described in my .gus.properties file?) > > > > > > > gus is strict about its data. we track pretty much everything. so, > > > for example, in order to put data in from an external database, or, to > > > mention source ids of an external database, the external database must > > > be known by gus. the two tables that hold this are: > > > SRes.ExternalDatabase and SRes.ExternalDatabaseRelease. The former > > > describes the DB, the latter the particular release of the DB, and it > > > points back to the former. The GBParser is asking you for a primary > > > key in the ExternalDatabaseRelease table so that all the data you load > > > will be associated with it. > > > > > > in the case of GenBank, we at cbil only store one version of it, which > > > we update periodically. so, for it, we set the 'version' attribute to > > > "continuous." for other DBs, we store multiple copies. in that case > > > we use a real version number, and create a new ExternalDatabaseRelease > > > row each time we load a new one in. > > > > > > one of the known weaknesses of the current GUS install process is that > > > we don't provide a bunch of standard databases as part of the data that > > > we load to get you off the ground. but, paul mooney has been handing > > > out an xml file which you can load with the UpdateGusFromXML plugin. > > > his mail is pj...@sa... > > > > > > that file only works for databases that you will only maintain one > > > release of. if you want to load multiple versions of a db (eg, pfam), > > > you will need to add new rows. > > > > > > >3) --algoinvo=s: What is this? (I looked at the docs but they talk > > about some invocation id. Is this to change the algorithm to be invoked?) > > > > > > > > > > > > > > > i see that michael answered this > > > > > > >Any help will be really appreciated > > > > > > > > > > > >thanks > > > >--Jinal > > > > > > > > > > > > > > > > > > > > > > > >------------------------------------------------------- > > > >This SF.Net email is sponsored by: SourceForge.net Broadband > > > >Sign-up now for SourceForge Broadband and get the fastest > > > >6.0/768 connection for only $19.95/mo for the first 3 months! > > > >http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > > > >_______________________________________________ > > > >Gusdev-gusdev mailing list > > > >Gus...@li... > > > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > > This SF.Net email is sponsored by: Oracle 10g > > > Get certified on the hottest thing ever to hit the market... Oracle 10g. > > > Take an Oracle 10g class now, and we'll give you the exam FREE. > > > http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click > > > _______________________________________________ > > > Gusdev-gusdev mailing list > > > Gus...@li... > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: Oracle 10g > Get certified on the hottest thing ever to hit the market... Oracle 10g. > Take an Oracle 10g class now, and we'll give you the exam FREE. > http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
