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

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Yes.  Is this a 3.5 install?  These rules should have been created  
automatically.  There should be a $GUS_HOME/config/SchemaInstall- 
objects.sql file (or similar, if using the trunk) that logged all  
created objects/rules in the database-- are the rules in that file?   
If so, then the rule was created but incorrectly-- please file a bug  
if that's the case, and make sure to submit that file.

--Mike

On Dec 8, 2005, at 1:53 PM, Mark S. Heiges wrote:

> 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
>>
>>
>
>
>
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