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

[Mark S. H. <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