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Re: [Gusdev-gusdev] LoadNRDB newbie questions:
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From: Deborah F. P. <pi...@pc...> - 2003-05-29 19:45:32
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Hi Michael, These are the arguments that I used: --temp_login "pinney" --sourceDB 'GENBANK (NRDB):gb,EMBL DATA LIBRARY (NRDB):emb,DDBJ (NRDB):dbj,NBRF PIR (NRDB):pir,PROTEIN RESEARCH FOUNDATION (NRDB):prf,SWISS-PROT (NRDB):sp,BROOKHAVEN PROTEIN DATA BANK (NRDB):pdb,PATENTS (NRDB):pat,GENINFO BACKBONE ID (NRDB):bbs,GENERAL DATABASE IDENTIFIER (NRDB):gnl,NCBI REFERENCE SEQUENCE (NRDB):ref,LOCAL SEQUENCE IDENTIFIER:lcl,GENPEPT:genpept' --temp_password "xxxxxxx" --dbi_str 'dbi:Oracle:host=erebus.pcbi.upenn.edu;sid=gusdev' --gitax /ptolemy/gi_taxid_prot.dmp --nrdb /ptolemy/nr --extDbRelId 4194 --maketemp --plugin --delete The temp table is necessary for updating and even though you are only filling the table for the first time, you will need to include this. I think Jonathan answered the general questions about temp tables and why you might need them. The plugin actually truncates, drops, creates the nrdbtemp table and grants select permission to gusrw. That last one is an error that will be fixed in the future but for now you may want to hard code the appropriate login. I included --dbi_str because I thought that this could and might vary from your config file. The plugin runs in three sections, make the temp table, insert and update into NRDBEntry and ExternalAASequence, and delete obsolete entries in those two tables. Each section can be run separately and each is specified as --maketemp, --plugin, --delete. They should be run sequentially but for testing and in case of failure, they can be run at separate times. You could skip the --delete. I hope this helps. Debbie On Thu, 29 May 2003, MICHAEL LUCHTAN wrote: > Hello All: > I am trying to load the genbank nrdb database into GUS so that I will have > what I blast against in the db so that I can load blast similarities. > I have some questions regarding this plugin. > What is the temp table for? Why is it necessary? Why must I proide > another login to the database to create this table? I would think that it > could just use the login/information provided in my gus config file. > > Can anyone clarify the args --plugin, and --maketemp? i.e. what happens > if these are/are not provided? > > Which arguements are required? > > > Also, I have tried to run the plugin with the following command: > ga GUS::Common::Plugin::LoadNRDB --testnumber1=10 --testnumber2=10 > --nrdb=/scratch/NCBI/nr > --gitax=/scratch/luchtan/taxonomy/gi_taxid_prot.dmp --extDbRelId=135 > --verbose --maketemp --temp_login=luchtan --temp_password=******* > --dbi_str=dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS > > But I get an error like this: > > Thu May 29 12:01:35 2003 **COMMIT TURNED OFF** > > Thu May 29 12:01:35 2003 Testing on 10 insertions > into temp table > > Thu May 29 12:01:35 2003 Testing on 10 insertions > into NRDBEntry/ExternalAASequence > > There are 0 entries in the database hash > Thu May 29 12:02:40 2003 There are 2900500 gi to taxon_id pairs > > DBI->connect(host=mango.ctegd.uga.edu) failed: ORA-12154: TNS:could not > resolve service name (DBD ERROR: OCIServerAttach) at > /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 216 > > > sqlExec: > UPDATE Core.AlgorithmInvocation > SET > end_time = SYSDATE, > row_alg_invocation_id = ?, > modification_date = SYSDATE > WHERE algorithm_invocation_id = ? > bindValues (245, 245) > DbiHandle:sqlExec:insert succeeded 1 row(s) > Can't call method "do" on an undefined value at > /home/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 219. > > > > I might be kind of "fresh" with regards to my interaction with Oracle, so > I am not sure if the dbi_str argument is in the correct format. Can > anyone help me with this? > > > Michael Luchtan > http://www.cs.uga.edu/~luchtan > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: eBay > Get office equipment for less on eBay! > http://adfarm.mediaplex.com/ad/ck/711-11697-6916-5 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
