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Re: [Gusdev-gusdev] GBParser
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From: Steve F. <sfi...@pc...> - 2004-05-20 17:52:47
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ok, i looked into this. the algoinvo arg is a bit arcane. ignore it. (whenever a plugin is run we track that fact in GUS. that is done with the AlgorithmInvocation tables among others. this arg allows you to restart a run of the plugin and have it be identified as a part of its original AlgorithmInvocation). steve MICHAEL LUCHTAN wrote: >Well, good thing I already loaded our data! Guess we need to update CVS. > >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 >> >> >> > > > >------------------------------------------------------- >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 > > |
