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Re: [GUSDEV] RES: Re: Inserting Sequence Features - Problem with a big reference.
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From: Ricardo B. <rb...@gm...> - 2005-12-13 16:46:55
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Hi Mark,
I executed the ISFU plugin, but now I am taking another error. All tables
are empty. Do you know to say me what is happening? The error follows
below:
[rbalbi1@crithidia bancos]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
$GUS_HOME/config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt
--fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer
"2005-12-06" -- sqlVerbose --commit
Tue Dec 13 14:38:54 2005 ARG algoinvo 1
Tue Dec 13 14:38:54 2005 ARG comment
Tue Dec 13 14:38:54 2005 ARG commit 0
Tue Dec 13 14:38:54 2005 ARG debug 0
Tue Dec 13 14:38:54 2005 ARG defaultOrganism
Tue Dec 13 14:38:54 2005 ARG extDbName Kinetoplastida_nt
Tue Dec 13 14:38:54 2005 ARG extDbRlsVer 2005-12-06
Tue Dec 13 14:38:54 2005 ARG fileFormat genbank
Tue Dec 13 14:38:54 2005 ARG gff2GroupTag
Tue Dec 13 14:38:54 2005 ARG group
Tue Dec 13 14:38:54 2005 ARG gusconfigfile
/GUS/gus_home/config/gus.config
Tue Dec 13 14:38:54 2005 ARG handlerExternalDbs
Tue Dec 13 14:38:54 2005 ARG help
Tue Dec 13 14:38:54 2005 ARG helpHTML
Tue Dec 13 14:38:54 2005 ARG inputFileExtension
Tue Dec 13 14:38:54 2005 ARG inputFileOrDir kinetoplastida_nt
Tue Dec 13 14:38:54 2005 ARG makeSourceids
Tue Dec 13 14:38:54 2005 ARG mapFile
/GUS/gus_home/config/genbank2gus.xml
Tue Dec 13 14:38:54 2005 ARG naSequenceSubclass
Tue Dec 13 14:38:54 2005 ARG project
Tue Dec 13 14:38:54 2005 ARG seqIdColumn source_id
Tue Dec 13 14:38:54 2005 ARG seqSoTerm
Tue Dec 13 14:38:54 2005 ARG seqType
Tue Dec 13 14:38:54 2005 ARG soCvsVersion
Tue Dec 13 14:38:54 2005 ARG sqlVerbose 0
Tue Dec 13 14:38:54 2005 ARG testNumber
Tue Dec 13 14:38:54 2005 ARG user
Tue Dec 13 14:38:54 2005 ARG verbose 0
Tue Dec 13 14:38:54 2005 ARG veryVerbose 0
Tue Dec 13 14:38:54 2005 AlgInvocationId 51
Tue Dec 13 14:38:54 2005 COMMIT commit off
Tue Dec 13 14:38:56 2005 Processing file 'kinetoplastida_nt'...
DBD::Pg::st execute failed: ERROR: duplicate key violates unique constrain=
t
"pk_nasequenceimp"
ERROR:
SQL ERROR!! involving
INSERT INTO DoTS.ExternalNASequence ( sequence, group_read, user_read,
other_write, modification_date, subclass_view, row_group_id, user_write,
other_read, group_write, source_id, external_database_release_id, c_count,
g_count, taxon_id, name, row_user_id, description, a_count, t_count, length=
,
row_project_id, row_alg_invocation_id, sequence_version, na_sequence_id )
VALUES ( ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?=
,
?, ?, ?, ?, ?, ? )
Values:
CAAGGAGGCGGAGAGAATAGAGGGGAGAAAAGAACGGCTTGGGTTTGTCTCTTTATTATACTTTTTATTGTCTTT=
AGTTCCTTGTGCCTCTTGATATGAATTTTTTCGCTACGCTCGATGCGACCGTCTTGAGACAATTGGCTCTGAATT=
TCTGACGCAAACGCTCCTCCGTATGACTGTTAGGGGCGGTGTCTTTTTACTTTCACGCCTGCGCACGTTTGTCTT=
TATTTTGTTCTGCTGTTTGCGTGTATTTCTGTTTGTGTATGCTTGTGCGCTTTTGCTGCATGGGGTGGTGGTGGT=
TGAAGTCCGTCAAAGTGCCTGTCGCTTTTTTTTTCTCAGGGTTTCTTTTTCTTGCTGGAGGTGCAGTGAAGATTT=
GTTTTGCTTTGCGAGGGGTGGAAAGCGTGAAACACACGCCTCGGTCCTGGCGGTAGAGGGAGGGGCGAGGGGTGG=
AGATTTATTTGGGGGAAAAGTGTGCTGCCGATGAGTTTTTTGCCGGATCGGGATCACGGGGAGGAGGAGGTTTGT=
GACAGTGAACATACGGCACCGCCGCCACAAGAGCAGCGACAGTTGCCTCCCGTGGCTGCGGCGTCTAGCGTGCCG=
CTGCGGCCGCGCGTTTCCCATGAAGAGCCACTCACCGCCACGTGTGACGCCCAGGCGGCGGTTTCTCGTGCTGGC=
GGTGCTGGCGACGGTGGCGGCAACGTCAAGGTTCGCAAGCTGCGGATTTTTGATGACATCACCACCACCACCTCT=
TCTTCTGAGATGTCTGGAAGGCATGTCAGCACAATTAAGGGGCACTCTGTCCTCAGGCACGCGTTACCGCCGCCT=
CGGGAGAGCGATATTGCGGAACAAAATATGTCGAGTACTGTTGCGCCAACGCAACCTTCATCCTCGACCCAAGTC=
GCTCCGGAGGCAGTGGCAGCACCCGTGAGTCTTCATCAAGTGGAAATCTCCGTCAGCAACCGAGCGGGCGACGCG=
CCTGTTGCACCGGCGGAGGTGAGGTCATCGCGGGGACCAGAAGGGAGGGCTTGGCGAGGCAGCCCGCCGGGAAGT=
CGCGGCGACGCGCATGGTGAATATACTGTAGTGAGCATGAGTAAGAAGTTTAGTGAAAAAATAGAGGAATTCTGG=
GAATTTGGGACGCAGGCGGACACGCACGTTCTTGTGATGTTTGTTTCTTCAGTTTTGTCGTTTGTATTGACTGTC=
GTTGCGGCACCTCTCTCCCAGTTGGACAT,
1, 1, 0, ExternalNASequence, 1, 1, 1, 1, NW_001081897, 177, 282, 384, 79703=
,
NW_001081897, 1, Trypanosoma cruzi strain CL Brener tcruzi_1047053482831,
whole genome shotgun sequence., 231, 332, 1229, 1, 51, 1, 3 at
/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9f=
c)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
DoTS.ExternalNASequ...') called at
/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede=
9fc)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY(0xa5be7ec)',
'\x{a} INSERT INTO DoTS.ExternalNASequence ( sequence, group_r...')
called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::ExternalNASequenc=
e=3DHASH(0xa4dbff8)',
'HASH(0xa5a7fec)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 613
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::ExternalNASequence=3DHASH(0=
xa4dbff8)')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa=
4dbff8)')
called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
535
GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Suppo=
rted::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)',
'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
326
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x90f15ac)',
'HASH(0xa031ae8)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x90d0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x90d0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x90d0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x90d0c20)',
'ARRAY(0x90e46d8)') called at /GUS/gus_home/bin/ga line 11
STACK TRACE:
at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9f=
c)',
'\x{a} SQL ERROR!! involving\x{a} \x{a} INSERT INTO
DoTS.ExternalNASequ...') called at
/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede=
9fc)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY(0xa5be7ec)',
'\x{a} INSERT INTO DoTS.ExternalNASequence ( sequence, group_r...')
called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::ExternalNASequenc=
e=3DHASH(0xa4dbff8)',
'HASH(0xa5a7fec)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 613
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::ExternalNASequence=3DHASH(0=
xa4dbff8)')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa=
4dbff8)')
called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
535
GUS::Supported::Plugin::InsertSequenceFeatures::processSequence('GUS::Suppo=
rted::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)',
'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
326
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DHASH(0x90f15ac)',
'HASH(0xa031ae8)') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 549
eval {...} called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 541
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::Gu=
sApplication=3DHASH(0x90d0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplica=
tion=3DHASH(0x90d0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=
=3DHASH(0x90d0c20)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=
=3DHASH(0x90d0c20)',
'ARRAY(0x90e46d8)') called at /GUS/gus_home/bin/ga line 11
2005/12/13, Mark S. Heiges <mh...@ug...>:
>
> No need to do it manually, those clever GUS developers made a plugin
> for this. Do
>
> ga GUS::Supported::Plugin::InsertSequenceFeaturesUndo --mapFile
> $GUS_HOME/config/genbank2gus.xml --algInvocationId 26 --commit
>
> (Change the mapFile and the algInvocationId
> (dots.externalnasequence.row_alg_invocation_id) arguments as needed.
> The values I'm giving are based on the log you posted in your
> 2005-12-06 email).
>
> On Dec 13, 2005, at 8:33 AM, Ricardo Balbi wrote:
>
> > Hi,
> > I obtained to create the rules and I think that now I go to
> > obtain to make the load. However, some registers had been inserted
> > in the previous executions of the ISF and are taking error of
> > primary key violated. Is there some way to undo what already was
> > made to execute the plugin again or I have to delete the rows
> > manually?
> >
> > thanks,
> > Ricardo
> >
> > 2005/12/9, Fabr=EDcio <fab...@de...>: Hello Ricardo and gus-
> > devers.
> >
> > I'm dealing with this same problem in my current Gus + Postgres
> > installation.
> >
> > My platform is:
> >
> > Postgres 8.1 in linux.
> >
> > I will follow mike's tip and see object.sql file to modify rules in
> > views.
> >
> > Best regards,
> >
> > Fabricio.
> >
> > -----Mensagem original-----
> > De: gus...@li...
> > [mailto: gus...@li...] Em nome de
> > gus...@li...
> > Enviada em: sexta-feira, 9 de dezembro de 2005 02:09
> > Para: gus...@li...
> > Assunto: Gusdev-gusdev digest, Vol 1 #741 - 1 msg
> >
> > Send Gusdev-gusdev mailing list submissions to
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> > Today's Topics:
> >
> > 1. Re: Inserting Sequence Features - Problem with a big reference.
> > (Michael Saffitz)
> >
> > --__--__--
> >
> > Message: 1
> > Cc: gus...@li...
> > From: Michael Saffitz < msa...@pc...>
> > Subject: Re: [GUSDEV] Inserting Sequence Features - Problem with a big
> > reference.
> > Date: Thu, 8 Dec 2005 14:39:12 -0500
> > To: Ricardo Balbi <rb...@gm... >
> >
> >
> > On Dec 8, 2005, at 2:34 PM, Ricardo Balbi wrote:
> >
> > > Yes Michael, this is a 3.5 install.
> > > The file exists and the rules too, but they had not been created. I
> > > created one manually.
> > > I will file a bug and submit the sql file.
> > >
> >
> > Hmmm... Ok. Do you still have the log from the install? I believe
> > this has worked for others, so it may be particular to your setup.
> > Please include in the bug report your version of Postgres, platform,
> > etc.
> >
> > > Do you have a file with all the rules to create in my database ?
> >
> > Yes, that object.sql file should have everything that belongs in the
> > database.
> >
> > --Mike
> >
> >
> >
> > --__--__--
> >
> > _______________________________________________
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> >
> >
> > End of Gusdev-gusdev Digest
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