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Re: [GUSDEV] Out of Memory while loading Taxonomy data
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From: Kumar, S. <San...@ng...> - 2006-07-12 16:27:32
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Hi Group,
As Josef suggested in his previous mail, I deleted the entry on line
number (given in the error message)from the merged.dmp. And when I ran
the loading it certainly passed the previous error point.
So, I think that the Josef's suggestion worked.
But I am getting a new type of error message, provided below. Can some
one pl. help me in understanding/resolving the error message.
Thanks
Sanjeev
------------------------------------------------------------------------
---------------------------------
********select d.name,t2.name as superclass,t1.name as subclass from
CORE.TableInfo t1,CORE.TableInfo t2, CORE.DatabaseInfo d where t
2.table_id =3D t1.view_on_table_id and t1.name not like '%Ver' and
d.database_id =3D t2.database_id********select * from TESS.MoietyImp
WHERE taxon_id =3D 525455
********select * from DoTS.NASequenceImp
WHERE taxon_id =3D 525455
Insufficient permission to retrieve GUS::Model::DoTS::NASequenceImp
Child of GUS::Model::SRes::Taxon
********select * from DoTS.AASequenceImp
WHERE taxon_id =3D 525455
********select * from Study.BioMaterialImp
WHERE taxon_id =3D 525455
Wed Jul 12 12:03:38 2006 Taxon_id =3D
GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D
GUS::Model::SRes::Taxon=3DHAS H(0x9ee9e54)
DBD::Oracle::db do failed: ORA-02292: integrity constraint
(DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD ERROR:
OCIStm tExecute) [for Statement "DELETE FROM
SRes.Taxon
WHERE taxon_id =3D 525455
"] at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 119, <MERGED> line 5476.
ERROR:
SQL ERROR!! involving
DELETE FROM SRes.Taxon
WHERE taxon_id =3D 525455
at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
166
=20
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9e7c=
b
84)', '\x{a} SQL ERROR!! involving\x{a} DELETE FROM S
Res.Taxon \x{a}\x{9}WHERE tax...') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 120
=20
GUS::ObjRelP::DbiDbHandle::sqlexecIns('GUS::ObjRelP::DbiDbHandle=3DHASH(0=
x
9e7cb84)', 'DELETE FROM SRes.Taxon \x{a}\x{9}WHERE
taxon_id =3D 525455 \x{a}') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 583
=20
GUS::ObjRelP::DbiRow::removeFromDB('GUS::Model::SRes::Taxon=3DHASH(0xa166=
c
f8)') called at /home/oragus35/GUS/gus_home/lib/perl/
GUS/Model/GusRow.pm line 1658
=20
GUS::Model::GusRow::submit('GUS::Model::SRes::Taxon=3DHASH(0xa166cf8)')
called at /home/oragus35/GUS/gus_home/lib/perl/GUS/Supp
orted/Plugin/LoadTaxon.pm line 196
=20
GUS::Supported::Plugin::LoadTaxon::updateTaxonAndChildRows('GUS::Support
ed::Plugin::LoadTaxon=3DHASH(0x9defc2c)', 525455, 61030
7) called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadTaxon.pm
line 155
=20
GUS::Supported::Plugin::LoadTaxon::mergeTaxons('GUS::Supported::Plugin::
LoadTaxon=3DHASH(0x9defc2c)') called at /home/oragus35/
GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadTaxon.pm line 114
=20
GUS::Supported::Plugin::LoadTaxon::run('GUS::Supported::Plugin::LoadTaxo
n=3DHASH(0x9defc2c)', 'HASH(0xa08c2bc)') called at /hom
e/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
469
eval {...} called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 461
=20
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
:GusApplication=3DHASH(0x994f180)', 'GUS::Supported::Pl
ugin::LoadTaxon', 1) called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380
=20
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
ication=3DHASH(0x994f180)', 'GUS::Supported::Plugin::Lo
adTaxon') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288
=20
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x994f180)', 'GUS::Supported::Plugin::LoadTa
xon') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197
=20
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x994f180)', 'ARRAY(0x994f924)') called at /
home/oragus35/GUS/gus_home/bin/ga line 11
STACK TRACE:
at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
166
=20
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9e7c=
b
84)', '\x{a} SQL ERROR!! involving\x{a} DELETE FROM S
Res.Taxon \x{a}\x{9}WHERE tax...') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 120
=20
GUS::ObjRelP::DbiDbHandle::sqlexecIns('GUS::ObjRelP::DbiDbHandle=3DHASH(0=
x
9e7cb84)', 'DELETE FROM SRes.Taxon \x{a}\x{9}WHERE
taxon_id =3D 525455 \x{a}') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 583
=20
GUS::ObjRelP::DbiRow::removeFromDB('GUS::Model::SRes::Taxon=3DHASH(0xa166=
c
f8)') called at /home/oragus35/GUS/gus_home/lib/perl/
GUS/Model/GusRow.pm line 1658
=20
GUS::Model::GusRow::submit('GUS::Model::SRes::Taxon=3DHASH(0xa166cf8)')
called at /home/oragus35/GUS/gus_home/lib/perl/GUS/Supp
orted/Plugin/LoadTaxon.pm line 196
=20
GUS::Supported::Plugin::LoadTaxon::updateTaxonAndChildRows('GUS::Support
ed::Plugin::LoadTaxon=3DHASH(0x9defc2c)', 525455, 61030
7) called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadTaxon.pm
line 155
=20
GUS::Supported::Plugin::LoadTaxon::mergeTaxons('GUS::Supported::Plugin::
LoadTaxon=3DHASH(0x9defc2c)') called at /home/oragus35/
GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadTaxon.pm line 114
=20
GUS::Supported::Plugin::LoadTaxon::run('GUS::Supported::Plugin::LoadTaxo
n=3DHASH(0x9defc2c)', 'HASH(0xa08c2bc)') called at /hom
e/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
469
eval {...} called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 461
=20
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
:GusApplication=3DHASH(0x994f180)', 'GUS::Supported::Pl
ugin::LoadTaxon', 1) called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 380
=20
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
ication=3DHASH(0x994f180)', 'GUS::Supported::Plugin::Lo
adTaxon') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 288
=20
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x994f180)', 'GUS::Supported::Plugin::LoadTa
xon') called at
/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 197
=20
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
ion=3DHASH(0x994f180)', 'ARRAY(0x994f924)') called at /
home/oragus35/GUS/gus_home/bin/ga line 11
Thanks
Sanjeev
-----Original Message-----
From: Josef Jurek [mailto:ju...@cs...]=20
Sent: Wednesday, July 12, 2006 11:43 AM
To: gus...@li...; Kumar, Sanjeev
Cc: ju...@cs...
Subject: Re: [GUSDEV] Out of Memory while loading Taxonomy data
"Kumar, Sanjeev" <San...@ng...> writes:
>
> Hi Josef,
> thanks for your quick response, let me look for the same entry and=20
> delete it and then retry the loading.
>=20
> Thanks
> Sanjeev
Well, don't necessarily delete the "exact" entry, rather, delete the
entry that is on the line number indicated by your error message. I
would be interested if it is the same data or not though.
Josef
Josef Jurek, Ph.D.
Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...
voice: (773) 702-9559
fax: (773) 702-6648
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