Re: [Gusdev-gusdev] LoadNRDB newbie questions:

[Jonathan C. <cra...@pc...>]

Hi Michael-

MICHAEL LUCHTAN wrote:
> 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.

My recollection is that Deborah Pinney worked on this plugin most recently;
Debbie, please correct me if I'm wrong on that count.  I don't know without
looking at the code what the temp. table is used for, but there are a couple
of different reasons why it's desirable to allow the user to supply a
different login under which to create it:

1. Prevents temp. tables from cluttering (even if only temporarily) the
    main GUS namespaces and/or shared database logins (like the "GUSrw"
    login we often use at CBIL.)
2. In the same vein, it allows two different users who are both running
    LoadNRDB to avoid trying to create or modify the same table.
3. The login specified in the config. file might not necessarily have
    CREATE TABLE privileges, since these are not needed for most GUS
    operations.

> Can anyone clarify the args --plugin, and --maketemp?  i.e. what happens
> if these are/are not provided?
 >
> Which arguements are required?

These are all very good questions and the answers certainly aren't clear
from the documentation of the plugin's arguments.

> 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

Try the following two things (in this order, since the first item will
probably fix the problem):

1. Quote the DBI string on your plugin command line; your shell
    is probably trying to interpret the semicolon embedded therein.
    In other words, use the following argument for the dbi_str (single
    quotes should do the trick for csh/tcsh):

    --dbi_str='dbi:Oracle:host=mango.ctegd.uga.edu;sid=GUS'

2. Also double-check that your --dbi_str argument matches the "dbiDsn"
    parameter in your $GUS_CONFIG_FILE.  I'm not sure why the plugin
    makes you specify this value separately, since the code will almost
    certainly break if you specify an Oracle server different from the
    one that hosts GUS (i.e., the one identified in the config. file).

Jonathan