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Re: [GUSDEV] RES: Re: Inserting Sequence Features - Problem with a big reference.
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From: Steve F. <sfi...@pc...> - 2005-12-13 21:22:42
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the install of GUS should have made a primary key _sq, ie, a database=20
"sequence" that generates the next primary key for that table.
it looks like the na_sequence_id that is being written is 3.
is there any row in DoTS.NASequenceImp with a na_sequence_id of 3?
steve
Mark S. Heiges wrote:
> 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 (0xa5be7ec)'=
,=20
>> '\x{a} INSERT INTO DoTS.ExternalNASequence ( sequence,=20
>> group_r...') called at /GUS/gus_home/lib/perl/GUS/ ObjRelP/DbiRow.pm=20
>> 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/ DbiRow.pm=20
>> 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/ InsertSequenceFeatures.pm=20
>> 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 (0xa5be7ec)'=
,=20
>> '\x{a} INSERT INTO DoTS.ExternalNASequence ( sequence,=20
>> group_r...') called at /GUS/gus_home/lib/perl/GUS/ ObjRelP/DbiRow.pm=20
>> 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/ DbiRow.pm=20
>> 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/ InsertSequenceFeatures.pm=20
>> 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 =
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
>> > gus...@li...
>> >
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>> > than "Re: Contents of Gusdev-gusdev digest..."
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>> >
>> > Today's Topics:
>> >
>> > 1. Re: Inserting Sequence Features - Problem with a big referenc=
e.
>> > (Michael Saffitz)
>> >
>> > --__--__--
>> >
>> > Message: 1
>> > Cc: gus...@li...
>> > From: Michael Saffitz < msa...@pc...>
>> > Subject: Re: [GUSDEV] Inserting Sequence Features - Problem with a=20
>> 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
>> >
>> >
>> >
>> > --__--__--
>> >
>> > _______________________________________________
>> > Gusdev-gusdev mailing list
>> > Gus...@li...
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>> >
>> > End of Gusdev-gusdev Digest
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