Re: [GUSDEV] Inserting Sequence Features - Problem with a big reference.

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That's error looks specific for Postgres which I don't use. Someone  
else may need to help here. A quick search at google.com for   
"ERROR:  cannot insert into a view" or "You need an unconditional ON  
INSERT DO INSTEAD rule" turns up several clues.

-Mark

Mark Heiges
CryptoDB.org
C210 Life Sciences Building
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
TEL:  (706) 542-1447               FAX: (706) 542-3582

On Dec 8, 2005, at 6:04 AM, Ricardo Balbi wrote:

> Thanks Mark,
>
>   But now I have another error.
>   It 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" --commit
> Thu Dec  8 09:04:53 2005        ARG     algoinvo        1
> Thu Dec  8 09:04:53 2005        ARG     comment
> Thu Dec  8 09:04:53 2005        ARG     commit  1
> Thu Dec  8 09:04:53 2005        ARG     debug   0
> Thu Dec  8 09:04:53 2005        ARG     defaultOrganism
> Thu Dec  8 09:04:53 2005        ARG     extDbName        
> Kinetoplastida_nt
> Thu Dec  8 09:04:53 2005        ARG     extDbRlsVer     2005-12-06
> Thu Dec  8 09:04:53 2005        ARG     fileFormat      genbank
> Thu Dec  8 09:04:53 2005        ARG     gff2GroupTag
> Thu Dec  8 09:04:53 2005        ARG     group
> Thu Dec  8 09:04:53 2005        ARG     gusconfigfile   /GUS/ 
> gus_home/config/gus.config
> Thu Dec  8 09:04:53 2005        ARG     handlerExternalDbs
> Thu Dec  8 09:04:53 2005        ARG     help
> Thu Dec  8 09:04:53 2005        ARG     helpHTML
> Thu Dec  8 09:04:53 2005        ARG     inputFileExtension
> Thu Dec  8 09:04:53 2005        ARG     inputFileOrDir   
> kinetoplastida_nt
> Thu Dec  8 09:04:53 2005        ARG     makeSourceids
> Thu Dec  8 09:04:53 2005        ARG     mapFile /GUS/gus_home/ 
> config/genbank2gus.xml
> Thu Dec  8 09:04:53 2005        ARG     naSequenceSubclass
> Thu Dec  8 09:04:53 2005        ARG     project
> Thu Dec  8 09:04:53 2005        ARG     seqIdColumn     source_id
> Thu Dec  8 09:04:53 2005        ARG     seqSoTerm
> Thu Dec  8 09:04:53 2005        ARG     seqType
> Thu Dec  8 09:04:53 2005        ARG     soCvsVersion
> Thu Dec  8 09:04:53 2005        ARG     sqlVerbose      0
> Thu Dec  8 09:04:53 2005        ARG     testNumber
> Thu Dec  8 09:04:53 2005        ARG     user
> Thu Dec  8 09:04:53 2005        ARG     verbose 0
> Thu Dec  8 09:04:53 2005        ARG     veryVerbose     0
> Thu Dec  8 09:04:53 2005        AlgInvocationId 30
> Thu Dec  8 09:04:53 2005        COMMIT  commit on
> Thu Dec  8 09:04:55 2005        Processing file 'kinetoplastida_nt'...
> DBD::Pg::st execute failed: ERROR:  cannot insert into a view
> HINT:  You need an unconditional ON INSERT DO INSTEAD rule.
>
> ERROR:
>
>  SQL ERROR!! involving
>
>  Values: 4 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm  
> line 166
>         GUS::ObjRelP::DbiDbHandle::death 
> ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)', '\x{a} SQL ERROR!!  
> involving\x{a}  \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ 
> GUS/ObjRelP/DbiDbHandle.pm line 150
>         GUS::ObjRelP::DbiDbHandle::sqlExec 
> ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)',  
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0xb2b07b0)', 'ARRAY 
> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm  
> line 1813
>         GUS::Model::GusRow::version('GUS::Model::DoTS::Source=HASH 
> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm  
> line 1680
>         GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=HASH 
> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> InsertSequenceFeatures.pm line 731
>          
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)',  
> 'Bio::Seq::RichSeq=HASH(0xb0aa2d8)', 4, 177) called at /GUS/ 
> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm  
> line 330
>         GUS::Supported::Plugin::InsertSequenceFeatures::run 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)',  
> 'HASH(0xabe05b0)') 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::GusApplication=HASH(0x9c82c20)',  
> '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::GusApplication=HASH(0x9c82c20)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>         GUS::PluginMgr::GusApplication::doMajorMode 
> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>         GUS::PluginMgr::GusApplication::parseAndRun 
> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', 'ARRAY 
> (0x9c96700)') 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=HASH(0xaa904b0)', '\x{a} SQL ERROR!!  
> involving\x{a}  \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ 
> GUS/ObjRelP/DbiDbHandle.pm line 150
>         GUS::ObjRelP::DbiDbHandle::sqlExec 
> ('GUS::ObjRelP::DbiDbHandle=HASH(0xaa904b0)',  
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0xb2b07b0)', 'ARRAY 
> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm  
> line 1813
>         GUS::Model::GusRow::version('GUS::Model::DoTS::Source=HASH 
> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm  
> line 1680
>         GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=HASH 
> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> InsertSequenceFeatures.pm line 731
>          
> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)',  
> 'Bio::Seq::RichSeq=HASH(0xb0aa2d8)', 4, 177) called at /GUS/ 
> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm  
> line 330
>         GUS::Supported::Plugin::InsertSequenceFeatures::run 
> ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9ca3920)',  
> 'HASH(0xabe05b0)') 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::GusApplication=HASH(0x9c82c20)',  
> '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::GusApplication=HASH(0x9c82c20)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357
>         GUS::PluginMgr::GusApplication::doMajorMode 
> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)',  
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266
>         GUS::PluginMgr::GusApplication::parseAndRun 
> ('GUS::PluginMgr::GusApplication=HASH(0x9c82c20)', 'ARRAY 
> (0x9c96700)') called at /GUS/gus_home/bin/ga line 11
>
> Could you help me ?
>
> thanks again,
> Ricardo Balbi
>
>
>
>
>
> 2005/12/7, Mark S. Heiges <mh...@ug...>: One short term  
> solution is to adjust your local schema  "alter table
> SRes.Reference modify (author varchar2(4000))", or something like
> that, and then restart the loading.
>
> You can also file a feature request in the GUS Schema issue tracker
> to increase that column in a future release - https://
> www.cbil.upenn.edu/tracker.
>
> On Dec 6, 2005, at 6:48 PM, Ricardo Balbi wrote:
>
> > Hi,
> >
> >   I am trying to load kinetoplastida_nt, using
> > InsertSequenceFeatures plugin. But I am not obtaining.
> >   Kinetoplastida_nt has a register whose author field exceeds the
> > maximum size the table sres.reference .
> >
> >   How I must proceed to load this base?
> >
> >   It follows below the error:
> >
> > [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" --commit
> > Tue Dec  6 21:32:42 2005        ARG     algoinvo        1
> > Tue Dec  6 21:32:42 2005        ARG     comment
> > Tue Dec  6 21:32:42 2005        ARG     commit  1
> > Tue Dec  6 21:32:42 2005        ARG     debug   0
> > Tue Dec  6 21:32:42 2005        ARG     defaultOrganism
> > Tue Dec  6 21:32:42 2005        ARG     extDbName
> > Kinetoplastida_nt
> > Tue Dec  6 21:32:42 2005        ARG     extDbRlsVer     2005-12-06
> > Tue Dec  6 21:32:42 2005        ARG     fileFormat      genbank
> > Tue Dec  6 21:32:42 2005        ARG     gff2GroupTag
> > Tue Dec  6 21:32:42 2005        ARG     group
> > Tue Dec  6 21:32:42 2005        ARG     gusconfigfile   /GUS/
> > gus_home/config/gus.config
> > Tue Dec  6 21:32:42 2005        ARG     handlerExternalDbs
> > Tue Dec  6 21:32:42 2005        ARG     help
> > Tue Dec  6 21:32:42 2005        ARG     helpHTML
> > Tue Dec  6 21:32:42 2005        ARG     inputFileExtension
> > Tue Dec  6 21:32:42 2005        ARG     inputFileOrDir
> > kinetoplastida_nt
> > Tue Dec  6 21:32:42 2005        ARG     makeSourceids
> > Tue Dec  6 21:32:42 2005        ARG     mapFile /GUS/gus_home/
> > config/genbank2gus.xml
> > Tue Dec  6 21:32:42 2005        ARG     naSequenceSubclass
> > Tue Dec  6 21:32:42 2005        ARG     project
> > Tue Dec  6 21:32:42 2005        ARG     seqIdColumn     source_id
> > Tue Dec  6 21:32:42 2005        ARG     seqSoTerm
> > Tue Dec  6 21:32:42 2005        ARG     seqType
> > Tue Dec  6 21:32:42 2005        ARG     soCvsVersion
> > Tue Dec  6 21:32:42 2005        ARG     sqlVerbose      0
> > Tue Dec  6 21:32:42 2005        ARG     testNumber
> > Tue Dec  6 21:32:42 2005        ARG     user
> > Tue Dec  6 21:32:42 2005        ARG     verbose 0
> > Tue Dec  6 21:32:42 2005        ARG     veryVerbose     0
> > Tue Dec  6 21:32:42 2005        AlgInvocationId 26
> > Tue Dec  6 21:32:42 2005        COMMIT  commit on
> > Tue Dec  6 21:32:44 2005        Processing file  
> 'kinetoplastida_nt'...
> > DBD::Pg::st execute failed: ERROR:  value too long for type
> > character varying(1000)
> >
> > ERROR:
> >
> >  SQL ERROR!! involving
> >
> >     INSERT INTO SRes.Reference (  journal_or_book_name,
> > group_write, other_read, group_read, author, user_read,
> > row_user_id, reference_id, modification_date, other_write,
> > row_alg_invocation_id, row_project_id, row_group_id, title,
> > user_write )
> >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? )
> >  Values: Science 309 (5733), 409-415 (2005) PUBMED   16020725, 1,
> > 1, 1, El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D.,
> > Aggarwal,G., Tran,A.N., Ghedin,E., Worthey,E.A., Delcher,A.L.,
> > Blandin,G., Westenberger, S.J., Caler,E., Cerqueira,G.C.,
> > Branche,C., Haas,B., Anupama,A., Arner,E., Aslund,L., Attipoe,P.,
> > Bontempi,E., Bringaud,F., Burton,P., Cadag,E., Campbell,D.A.,
> > Carrington,M., Crabtree,J., Darban,H., da Silveira, J.F., de
> > Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T.,
> > Ferella,M., Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y.,
> > Kindlund,E., Klingbeil,M., Kluge,S., Koo,H., Lacerda,D.,
> > Levin, M.J., Lorenzi,H., Louie,T., Machado,C.R., McCulloch,R.,
> > McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S.,
> > Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M.,
> > Ramirez,J.L., Rinta,J., Robertson,L., Salzberg, S.L., Sanchez,D.O.,
> > Seyler,A., Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T.,
> > Tarleton,R., Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N.,
> > Wickstead,B., Wortman,J., White,O., Fraser,C.M., Stuart, K.D. and
> > Andersson,B., 1, 1, 6, 0, 26, 1, 1, The genome sequence of
> > Trypanosoma cruzi, etiologic agent of Chagas disease, 1 at /GUS/
> > gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
> >         GUS::ObjRelP::DbiDbHandle::death
> > ('GUS::ObjRelP::DbiDbHandle=HASH(0x91f4d14)', '\x{a} SQL ERROR!!
> > involving\x{a} \x{a}    INSERT INTO SRes.Reference (  j...') called
> > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150
> >         GUS::ObjRelP::DbiDbHandle::sqlExec
> > ('GUS::ObjRelP::DbiDbHandle=HASH(0x91f4d14)',
> > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8e826cc)', 'ARRAY
> > (0x8e82708)', '\x{a}    INSERT INTO SRes.Reference
> > (  journal_or_book_name, grou...') called at /GUS/gus_home/lib/perl/
> > GUS/ObjRelP/DbiRow.pm line 666
> >         GUS::ObjRelP::DbiRow::quote_and_insert
> > ('GUS::Model::SRes::Reference=HASH(0x987901c)', 'HASH(0x9889d48)')
> > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
> >         GUS::ObjRelP::DbiRow::insert
> > ('GUS::Model::SRes::Reference=HASH(0x987901c)') called at /GUS/
> > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
> >
> >
> > thanks,
> > Ricardo
>
>