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From: Ed R. <ero...@ug...> - 2006-07-12 15:04:42
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Can you send the actual error message? Is it a GUS error or an Oracle error. -ed ---- Original message ---- >Date: Wed, 12 Jul 2006 10:57:13 -0400 >From: "Kumar, Sanjeev" <San...@ng...> >Subject: [GUSDEV] Out of Memory while loading Taxonomy data >To: <gus...@li...> > >Hi Group, > I am getting 'out of memory' error while loading the Taxonomy data. > I remember Jian Lu got this error earlier, but I couldn't find any >solution in the archive. > Pl. suggest me to resolve the issue. > >Thanks >Sanjeev > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
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From: <ju...@cs...> - 2006-07-12 15:43:17
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"Kumar, Sanjeev" <San...@ng...> writes: > > Hi Josef, > thanks for your quick response, let me look for the same entry and > delete it and then retry the loading. > > 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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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
|
|
From: <ju...@cs...> - 2006-07-12 17:31:55
|
"Kumar, Sanjeev" <San...@ng...> writes: > > But I am getting a new type of error message, provided below. Can some > one pl. help me in understanding/resolving the error message. > > > GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D > GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54) > DBD::Oracle::db do failed: ORA-02292: integrity constraint > (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD ERROR:OCIStmtExecute) > [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. > [...] I ran into this very same error as well. What is happening is that LoadTaxon is attempting to delete obsolete taxonomy entries _however_ some of these taxonomy entries are still referenced by the TAXON_ID field of DoTS.NASequence. What LoadTaxon _should_ _do_ is update all places in DoTS.NASequence/DoTS.AASequence (and possibly other tables) so that obsolete taxonomy entries are replace in the tables that reference them _before_ LoadTaxon tries to delete them from SRes.Taxon. My jury-rig (and I do mean jury-rig) was to run a perl script on merged.dmp to convert each data line to a SQL line which might look like: update DoTS.ExternalAASequence set taxon_id = 255892 where taxon_id = 256194; thus, updating the taxon_id fields. When it comes to updating Taxonomy information LoadTaxon does not appear to be very robust. 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 |
|
From: <jl...@vb...> - 2006-07-12 17:52:26
|
What I did to update taxonomy is to use SQL commnds. Assume you only have taxon_id on DoTS.Sequence table. 1. Backup your old taxon_id SQL>CREATE TABLE DoTS.NASequenceTaxonID AS select a.na_sequence_id, a.taxon_id, b.ncbi_tax_id from dots.nasequence a, sres.taxon b where a.taxon_id=b.taxon_id; 2. Delete taxon_id on DoTS.Sequence table SQL>update dots.nasequence set taxon_id = null; 3. Delete taxonomy data SQL>delete from sres.taxonname; SQL>delete from sres.taxon; 4.Run plugin to load new taxonomy data 5.Restore taxon_id on DoTS.Sequence table SQL>update dots.nasequence s set taxon_id=(select b.taxon_id from dots.nasequencetaxonid a, sres.taxon b where a.ncbi_tax_id=b.ncbi_tax_id and a.na_sequence_id=s.na_sequence_id); On Wed, July 12, 2006 1:31 pm, Josef Jurek wrote: > > "Kumar, Sanjeev" <San...@ng...> writes: > >> >> But I am getting a new type of error message, provided below. Can some >> one pl. help me in understanding/resolving the error message. >> >> >> GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D >> GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54) >> DBD::Oracle::db do failed: ORA-02292: integrity constraint >> (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD >> ERROR:OCIStmtExecute) >> [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. [...] >> > > I ran into this very same error as well. What is happening > is that LoadTaxon is attempting to delete obsolete taxonomy entries > _however_ some of these taxonomy > entries are still referenced by the TAXON_ID field of DoTS.NASequence. > > What LoadTaxon _should_ _do_ is update all places > in DoTS.NASequence/DoTS.AASequence (and possibly other tables) so that > obsolete taxonomy entries are replace in the tables that reference them > _before_ LoadTaxon tries to delete them > from SRes.Taxon. > > My jury-rig (and I do mean jury-rig) was > to run a perl script on merged.dmp to convert each data line to a SQL line > which might look like: > > update DoTS.ExternalAASequence set taxon_id = 255892 where taxon_id = > 256194; > > > thus, updating the taxon_id fields. > > When it comes to updating Taxonomy information > LoadTaxon does not appear to be very robust. > > > 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 > > > > > > > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, > security? Get stuff done quickly with pre-integrated technology to make > your job easier Download IBM WebSphere Application Server v.1.0.1 based on > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: <pi...@pc...> - 2006-07-12 19:06:04
|
LoadTaxonomy was written to update taxon_id in child tables prior to deleting the row in taxon_id so I suspect that something else is happening, for example a group_write or group_id issue. Debbie Quoting Josef Jurek <ju...@cs...>: > > "Kumar, Sanjeev" <San...@ng...> writes: >> >> But I am getting a new type of error message, provided below. Can some >> one pl. help me in understanding/resolving the error message. >> >> >> GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D >> GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54) >> DBD::Oracle::db do failed: ORA-02292: integrity constraint >> (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD >> ERROR:OCIStmtExecute) >> [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. >> [...] > > I ran into this very same error as well. What is happening > is that LoadTaxon is attempting to delete obsolete > taxonomy entries _however_ some of these taxonomy > entries are still referenced by the TAXON_ID field > of DoTS.NASequence. > > What LoadTaxon _should_ _do_ is update all places > in DoTS.NASequence/DoTS.AASequence (and possibly > other tables) so that obsolete taxonomy entries > are replace in the tables that reference > them _before_ LoadTaxon tries to delete them > from SRes.Taxon. > > My jury-rig (and I do mean jury-rig) was > to run a perl script on merged.dmp to > convert each data line to a SQL line which > might look like: > > update DoTS.ExternalAASequence set taxon_id = 255892 where taxon_id > = 256194; > > thus, updating the taxon_id fields. > > When it comes to updating Taxonomy information > LoadTaxon does not appear to be very robust. > > 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 > > > > > > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: <ju...@cs...> - 2006-07-12 20:45:46
|
pi...@pc... (Debbie) writes: > > LoadTaxonomy was written to update taxon_id in child tables prior to deleting > the row in taxon_id so I suspect that something else is happening, for example > a group_write or group_id issue. No, the problem is as I describe. Yes, obviously the intent behind LoadTaxon would have been to update taxon_id in all child tables first, but this is not happening. LoadTaxon is broken. > >> GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54) > >> DBD::Oracle::db do failed: ORA-02292: integrity constraint > >> (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD > >> ERROR:OCIStmtExecute) > >> [for Statement "DELETE FROM SRes.Taxon WHERE taxon_id = 525455 > >> "] at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > >> line 119, <MERGED> line 5476. > >> [...] |
|
From: Kumar, S. <San...@ng...> - 2006-07-12 15:29:31
|
Hi Ed, It is a GUS error. The error message is, Out of Memory! Issuing Rollback() for database handle being DESTROY'd without explicit disconnect(), <MERGED> line 3263 Issuing Rollback() for database handle being DESTROY'd without explicit disconnect(), <MERGED> line 3263 Thanks Sanjeev -----Original Message----- From: Ed Robinson [mailto:ero...@ug...]=20 Sent: Wednesday, July 12, 2006 11:05 AM To: Kumar, Sanjeev; gus...@li... Subject: Re: [GUSDEV] Out of Memory while loading Taxonomy data Can you send the actual error message? Is it a GUS error or an Oracle error. -ed ---- Original message ---- >Date: Wed, 12 Jul 2006 10:57:13 -0400 >From: "Kumar, Sanjeev" <San...@ng...> >Subject: [GUSDEV] Out of Memory while loading Taxonomy data >To: <gus...@li...> > >Hi Group, > I am getting 'out of memory' error while loading the Taxonomy data. > I remember Jian Lu got this error earlier, but I couldn't find any=20 >solution in the archive. > Pl. suggest me to resolve the issue. > >Thanks >Sanjeev > > >----------------------------------------------------------------------- >-- Using Tomcat but need to do more? Need to support web services,=20 >security? >Get stuff done quickly with pre-integrated technology to make your job=20 >easier Download IBM WebSphere Application Server v.1.0.1 based on=20 >Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 12164 >2 _______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
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