[Gusdev-gusdev] using update option in submitrow and UpdateGusFromCla plugin

[sucheta T. <su...@vb...>]

Hi,

We have been trying to update some data into GUS using the SubmitRow plugin.
Apparently from the first description line it appears the --refresh option
updates the data, so we used the following option:

ga GUS::Common::Plugin::SubmitRow --tablename SRes::ExternalDatabase
--attrlist
 external_database_id,name,lowercase_name --valuelist "16^^^PfamA^^^pfama"
--ref
resh --verbose --commit

Instead of executing the sql statement as update it says: insert into.....

It gives the following error:
=============================

Wed Dec 17 14:31:26 2003        ALGINVID        98
Wed Dec 17 14:31:26 2003        COMMIT  commit on
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(SRES.PK_EXTERNALDA
TABASE) violated (DBD ERROR: OCIStmtExecute) [for Statement "
    INSERT INTO SRes.ExternalDatabase (  other_read, group_write,
group_read, lo
wercase_name, name, user_read, row_user_id, external_database_id,
modification_d
ate, other_write, row_project_id, row_alg_invocation_id, row_group_id,
user_writ
e )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with
ParamVal
ues: :p5='PfamA', :p6='1', :p3='1', :p12='1', :p7='1', :p1='1', :p8='16',
:p4='p
fama', :p10='1', :p9='0', :p13='1', :p11='98', :p2='1'] at
/home/apps/GUS/dev/gu
shome/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
==========================================================================

SO I tried another plugin UpdateGusFromCla
using the following option:

ga GUS::Common::Plugin::UpdateGusFromCla --tablename
SRes::ExternalDatabase --at
trlist external_database_id,name,lowercase_name --valuelist
"16^^^PfamA^^^pfama"
 --refresh --verbose --commit

It looks like the program ends normally, but the database does not get
updated.

Following is the output:
========================
Reading properties from /home/apps/GUS/dev/gushome/config/GUS-PluginMgr.prop
Reading properties from /home/apps/GUS/dev/.gus.properties
Wed Dec 17 14:58:55 2003        ALGINVID        102
Wed Dec 17 14:58:55 2003        ARGS    algoinvo        1
Wed Dec 17 14:58:55 2003        ARGS    attrlist       
external_database_id,nam
e,lowercase_name
Wed Dec 17 14:58:55 2003        ARGS    comment
Wed Dec 17 14:58:55 2003        ARGS    commit  1
Wed Dec 17 14:58:55 2003        ARGS    debug
Wed Dec 17 14:58:55 2003        ARGS    group
Wed Dec 17 14:58:55 2003        ARGS    gusconfigfile  
/home/apps/GUS/dev/.gus.
properties
Wed Dec 17 14:58:55 2003        ARGS    project
Wed Dec 17 14:58:55 2003        ARGS    refresh 1
Wed Dec 17 14:58:55 2003        ARGS    sqlVerbose
Wed Dec 17 14:58:55 2003        ARGS    tablename      
SRes::ExternalDatabase
Wed Dec 17 14:58:55 2003        ARGS    usage
Wed Dec 17 14:58:55 2003        ARGS    user
Wed Dec 17 14:58:55 2003        ARGS    valuelist       16^^^PfamA^^^pfama
Wed Dec 17 14:58:55 2003        ARGS    verbose 1
Wed Dec 17 14:58:55 2003        ARGS    veryVerbose
Wed Dec 17 14:58:55 2003        COMMIT  commit on
Wed Dec 17 14:58:55 2003        Result  primary key is found in database,
doing
update
name     PfamA
lowercase_name   pfama
Wed Dec 17 14:58:55 2003        RESULT

So, Now I am in doubt whether I am using the correct plugin(s).
Are there any plugins which does the database update job?Do I need to do
it at the SQL commandline.

Thanks

Sucheta
-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138