[Gusdev-gusdev] LoadNRDB newbie questions:

[MICHAEL L. <lu...@cs...>]

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