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Re: [GUSDEV] RES: Re: Inserting Sequence Features - Problem with a big reference.
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From: Mark S. H. <mh...@ug...> - 2005-12-13 19:39:47
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The 'pk_nasequenceimp' unique constraint prevents duplicate =20
na_sequence_id values in DoTS.NASequence. Off hand, I do not know why =20=
values are being duplicated.
Anyone else want to pitch in?
On Dec 13, 2005, at 11:46 AM, Ricardo Balbi wrote:
> Hi Mark,
>
> I executed the ISFU plugin, but now I am taking another error. All =20=
> tables are empty. Do you know to say me what is happening? The =20
> error follows below:
>
> [rbalbi1@crithidia bancos]$ ga =20
> GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/=20
> config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt --=20
> fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer =20
> "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 =20
> 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/=20
> 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 =20
> kinetoplastida_nt
> Tue Dec 13 14:38:54 2005 ARG makeSourceids
> Tue Dec 13 14:38:54 2005 ARG mapFile /GUS/gus_home/=20
> 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 =20
> constraint "pk_nasequenceimp"
>
> ERROR:
>
> SQL ERROR!! involving
>
> INSERT INTO DoTS.ExternalNASequence ( sequence, group_read, =20
> user_read, other_write, modification_date, subclass_view, =20
> row_group_id, user_write, other_read, group_write, source_id, =20
> external_database_release_id, c_count, g_count, taxon_id, name, =20
> row_user_id, description, a_count, t_count, length, row_project_id, =20=
> row_alg_invocation_id, sequence_version, na_sequence_id )
> VALUES ( ?, ?, ?, ?, now=20
> (), ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )
> Values: =20
> CAAGGAGGCGGAGAGAATAGAGGGGAGAAAAGAACGGCTTGGGTTTGTCTCTTTATTATACTTTTTATTG=20=
> TCTTTAGTTCCTTGTGCCTCTTGATATGAATTTTTTCGCTACGCTCGATGCGACCGTCTTGAGACAATTG=20=
> GCTCTGAATTTCTGACGCAAACGCTCCTCCGTATGACTGTTAGGGGCGGTGTCTTTTTACTTTCACGCCT=20=
> GCGCACGTTTGTCTTTATTTTGTTCTGCTGTTTGCGTGTATTTCTGTTTGTGTATGCTTGTGCGCTTTTG=20=
> CTGCATGGGGTGGTGGTGGTTGAAGTCCGTCAAAGTGCCTGTCGCTTTTTTTTTCTCAGGGTTTCTTTTT=20=
> CTTGCTGGAGGTGCAGTGAAGATTTGTTTTGCTTTGCGAGGGGTGGAAAGCGTGAAACACACGCCTCGGT=20=
> CCTGGCGGTAGAGGGAGGGGCGAGGGGTGGAGATTTATTTGGGGGAAAAGTGTGCTGCCGATGAGTTTTT=20=
> TGCCGGATCGGGATCACGGGGAGGAGGAGGTTTGTGACAGTGAACATACGGCACCGCCGCCACAAGAGCA=20=
> GCGACAGTTGCCTCCCGTGGCTGCGGCGTCTAGCGTGCCGCTGCGGCCGCGCGTTTCCCATGAAGAGCCA=20=
> CTCACCGCCACGTGTGACGCCCAGGCGGCGGTTTCTCGTGCTGGCGGTGCTGGCGACGGTGGCGGCAACG=20=
> TCAAGGTTCGCAAGCTGCGGATTTTTGATGACATCACCACCACCACCTCTTCTTCTGAGATGTCTGGAAG=20=
> GCATGTCAGCACAATTAAGGGGCACTCTGTCCTCAGGCACGCGTTACCGCCGCCTCGGGAGAGCGATATT=20=
> GCGGAACAAAATATGTCGAGTACTGTTGCGCCAACGCAACCTTCATCCTCGACCCAAGTCGCTCCGGAGG=20=
> CAGTGGCAGCACCCGTGAGTCTTCATCAAGTGGAAATCTCCGTCAGCAACCGAGCGGGCGACGCGCCTGT=20=
> TGCACCGGCGGAGGTGAGGTCATCGCGGGGACCAGAAGGGAGGGCTTGGCGAGGCAGCCCGCCGGGAAGT=20=
> CGCGGCGACGCGCATGGTGAATATACTGTAGTGAGCATGAGTAAGAAGTTTAGTGAAAAAATAGAGGAAT=20=
> TCTGGGAATTTGGGACGCAGGCGGACACGCACGTTCTTGTGATGTTTGTTTCTTCAGTTTTGTCGTTTGT=20=
> ATTGACTGTCGTTGCGGCACCTCTCTCCCAGTTGGACAT, 1, 1, 0, =20
> ExternalNASequence, 1, 1, 1, 1, NW_001081897, 177, 282, 384, 79703, =20=
> NW_001081897, 1, Trypanosoma cruzi strain CL Brener =20
> tcruzi_1047053482831, whole genome shotgun sequence., 231, 332, =20
> 1229, 1, 51, 1, 3 at /GUS/gus_home/lib/perl/GUS/ObjRelP/=20
> DbiDbHandle.pm line 166
> GUS::ObjRelP::DbiDbHandle::death=20
> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', '\x{a} SQL ERROR!! =20
> involving\x{a} \x{a} INSERT INTO DoTS.ExternalNASequ...') called =20=
> at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
> GUS::ObjRelP::DbiDbHandle::sqlExec=20
> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', =20
> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY=20
> (0xa5be7ec)', '\x{a} INSERT INTO DoTS.ExternalNASequence =20
> ( sequence, group_r...') called at /GUS/gus_home/lib/perl/GUS/=20
> ObjRelP/DbiRow.pm line 666
> GUS::ObjRelP::DbiRow::quote_and_insert=20
> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)', 'HASH=20
> (0xa5a7fec)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/=20
> DbiRow.pm line 613
> GUS::ObjRelP::DbiRow::insert=20
> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /=20=
> GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
> GUS::Model::GusRow::submit=20
> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /=20=
> GUS/gus_home/lib/perl/GUS/Supported/Plugin/=20
> InsertSequenceFeatures.pm line 535
> =20
> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence=20
> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20=
> 'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at /GUS/gus_home/=20=
> lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 326
> GUS::Supported::Plugin::InsertSequenceFeatures::run=20
> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20=
> 'HASH(0xa031ae8)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20
> GusApplication.pm line 549
> eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20
> GusApplication.pm line 541
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/=20=
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
> GUS::PluginMgr::GusApplication::doMajorMode_Run=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
> GUS::PluginMgr::GusApplication::doMajorMode=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
> GUS::PluginMgr::GusApplication::parseAndRun=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', 'ARRAY=20
> (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=20
> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', '\x{a} SQL ERROR!! =20
> involving\x{a} \x{a} INSERT INTO DoTS.ExternalNASequ...') called =20=
> at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
> GUS::ObjRelP::DbiDbHandle::sqlExec=20
> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9ede9fc)', =20
> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xa5bcd8c)', 'ARRAY=20
> (0xa5be7ec)', '\x{a} INSERT INTO DoTS.ExternalNASequence =20
> ( sequence, group_r...') called at /GUS/gus_home/lib/perl/GUS/=20
> ObjRelP/DbiRow.pm line 666
> GUS::ObjRelP::DbiRow::quote_and_insert=20
> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)', 'HASH=20
> (0xa5a7fec)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/=20
> DbiRow.pm line 613
> GUS::ObjRelP::DbiRow::insert=20
> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /=20=
> GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
> GUS::Model::GusRow::submit=20
> ('GUS::Model::DoTS::ExternalNASequence=3DHASH(0xa4dbff8)') called at /=20=
> GUS/gus_home/lib/perl/GUS/Supported/Plugin/=20
> InsertSequenceFeatures.pm line 535
> =20
> GUS::Supported::Plugin::InsertSequenceFeatures::processSequence=20
> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20=
> 'Bio::Seq::RichSeq=3DHASH(0xa4fc60c)', 177) called at /GUS/gus_home/=20=
> lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line 326
> GUS::Supported::Plugin::InsertSequenceFeatures::run=20
> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x90f15ac)', =20=
> 'HASH(0xa031ae8)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20
> GusApplication.pm line 549
> eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/=20
> GusApplication.pm line 541
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at /GUS/=20=
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459
> GUS::PluginMgr::GusApplication::doMajorMode_Run=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
> GUS::PluginMgr::GusApplication::doMajorMode=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', =20
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/=20
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
> GUS::PluginMgr::GusApplication::parseAndRun=20
> ('GUS::PluginMgr::GusApplication=3DHASH(0x90d0c20)', 'ARRAY=20
> (0x90e46d8)') called at /GUS/gus_home/bin/ga line 11
>
> 2005/12/13, Mark S. Heiges <mh...@ug...>: No need to do it =20
> 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 =20=
> 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 =20
> reference.
> > (Michael Saffitz)
> >
> > --__--__--
> >
> > Message: 1
> > Cc: gus...@li...
> > From: Michael Saffitz < msa...@pc...>
> > Subject: Re: [GUSDEV] Inserting Sequence Features - Problem with =20
> 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 =20
> 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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