Re: [GUSDEV] LoadNRDB error

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Thanks Michael, it worked. But shouldn't this lines from the --help be
updated then?

The help file from LoadNRDB prints:

  --dbiStr *string*

        server and machine for temp table, e.g.
        dbi:Oracle:host=3Derebus.pcbi.upenn.edu;sid=3Dgusdev

Shouldn't that line be corrected?

Another thing, I've been trying to update sres.externaldatabase table
with no success.

$ ga GUS::Supported::Plugin::InsertExternalDatabase --name tpg --commit

Thu Nov  3 14:07:35 2005        ARG     algoinvo        1
Thu Nov  3 14:07:35 2005        ARG     comment
Thu Nov  3 14:07:35 2005        ARG     commit  1
Thu Nov  3 14:07:35 2005        ARG     debug   0
Thu Nov  3 14:07:35 2005        ARG     group
Thu Nov  3 14:07:35 2005        ARG     gusconfigfile   /gus/GUS/gus.proper=
ties
Thu Nov  3 14:07:35 2005        ARG     help
Thu Nov  3 14:07:35 2005        ARG     helpHTML
Thu Nov  3 14:07:35 2005        ARG     name    tpg
Thu Nov  3 14:07:35 2005        ARG     project
Thu Nov  3 14:07:35 2005        ARG     sqlVerbose      0
Thu Nov  3 14:07:35 2005        ARG     user
Thu Nov  3 14:07:35 2005        ARG     verbose 0
Thu Nov  3 14:07:35 2005        ARG     veryVerbose     0
Thu Nov  3 14:07:35 2005        AlgInvocationId 63
Thu Nov  3 14:07:35 2005        COMMIT  commit on
DBD::Pg::st execute failed: ERROR:  duplicate key violates unique
constraint "pk_externaldatabase"

ERROR:

 SQL ERROR!! involving

    INSERT INTO SRes.ExternalDatabase (  group_write, other_read,
group_read, name, user_read, row_user_id, external_database_id,
modification_date, other_write, row_alg_invocation_id, row_project_id,
row_group_id, user_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ? )
 Values: 1, 1, 1, tpg, 1, 1, 21, 0, 63, 1, 1, 1 at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(=
0x9100274)','\x{a}
SQL ERROR!! involving\x{a} \x{a}    INSERT INTO
SRes.ExternalDataba...') called at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHAS=
H(0x9100274)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x9691974)','ARRAY(0x96=
91a10)','\x{a}
   INSERT INTO SRes.ExternalDatabase (  group_write, other_...')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalD=
atabase=3DHASH(0x96831cc)','HASH(0x9682184)')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
        GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=3D=
HASH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
        GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=3DHA=
SH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDat=
abase.pm
line 103
        GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported=
::Plugin::InsertExternalDatabase=3DHASH(0x8e4b32c)','HASH(0x9616d54)')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 520
        eval {...} called at
/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 512
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExte=
rnalDatabase',1)
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 430
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalData=
base')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 337
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalDatabase=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 246
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','ARRAY(0x8e46678)')
called at /gus/GUS/gus_home/bin/ga line 11

STACK TRACE:
 at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
        GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(=
0x9100274)','\x{a}
SQL ERROR!! involving\x{a} \x{a}    INSERT INTO
SRes.ExternalDataba...') called at
/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
        GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHAS=
H(0x9100274)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x9691974)','ARRAY(0x96=
91a10)','\x{a}
   INSERT INTO SRes.ExternalDatabase (  group_write, other_...')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
        GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::ExternalD=
atabase=3DHASH(0x96831cc)','HASH(0x9682184)')
called at /gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
        GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::ExternalDatabase=3D=
HASH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
        GUS::Model::GusRow::submit('GUS::Model::SRes::ExternalDatabase=3DHA=
SH(0x96831cc)')
called at /gus/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDat=
abase.pm
line 103
        GUS::Supported::Plugin::InsertExternalDatabase::run('GUS::Supported=
::Plugin::InsertExternalDatabase=3DHASH(0x8e4b32c)','HASH(0x9616d54)')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 520
        eval {...} called at
/gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 512
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plugi=
nMgr::GusApplication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExte=
rnalDatabase',1)
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 430
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalData=
base')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 337
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','GUS::Supported::Plugin::InsertExternalDatabase=
')
called at /gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 246
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApp=
lication=3DHASH(0x8e32c18)','ARRAY(0x8e46678)')
called at /gus/GUS/gus_home/bin/ga line 11

I uploaded to this table a ExternalDatabases.xml archive, using
LoadGusXml. From what I could understand from that error, seems that
id was supplied to another entry (and indeed it was). I guess what is
happening is some kind of conflict between the entries I uploaded in
this tables and the new entries I'm trying to submit. I looked for any
conflicts among the entries I need to create (nr, tpe, tpd, tpg and a
few others) and the contents of the xml file, and I couldn't find any
duplicate entries.

Thanks again for the quick replies,

Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)