Menu
▾
▴
gusdev-gusdev
|
From: Ricardo B. <rb...@gm...> - 2005-12-06 23:48:49
|
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=3DHASH(0x91f4d1=
4)',
'\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=3DHASH(0x91f4=
d14)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(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=3DHASH(=
0x987901c)',
'HASH(0x9889d48)') called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 613
GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::Reference=3DHASH(0x987901c)=
')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
thanks,
Ricardo
|
|
From: Mark S. H. <mh...@ug...> - 2005-12-07 02:38:54
|
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 |
|
From: Ricardo B. <rb...@gm...> - 2005-12-08 11:04:36
|
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=3DHASH(0xaa904b=
0)',
'\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=3DHASH(0xaa90=
4b0)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY(0xa148314)') call=
ed
at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1813
GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1680
GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
731
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'Bio::Seq::RichSeq=3DHASH(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=3DHASH(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::Gu=
sApplication=3DHASH(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::GusApplica=
tion=3DHASH(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=
=3DHASH(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=
=3DHASH(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=3DHASH(0xaa904b=
0)',
'\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=3DHASH(0xaa90=
4b0)',
'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY(0xa148314)') call=
ed
at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1813
GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1680
GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH(0xb180fe0)')
called at
/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm line
731
GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees('GUS::S=
upported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)',
'Bio::Seq::RichSeq=3DHASH(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=3DHASH(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::Gu=
sApplication=3DHASH(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::GusApplica=
tion=3DHASH(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=
=3DHASH(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=
=3DHASH(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=3DHASH(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=3DHASH(0x91f4d14)',
> > 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(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=3DHASH(0x987901c)', 'HASH(0x9889d48)')
> > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613
> > GUS::ObjRelP::DbiRow::insert
> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)') called at /GUS/
> > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692
> >
> >
> > thanks,
> > Ricardo
>
>
|
|
From: Mark S. H. <mh...@ug...> - 2005-12-08 18:54:14
|
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 > > |
|
From: Michael S. <msa...@pc...> - 2005-12-08 19:02:59
|
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 >> >> > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through > log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD > SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Ricardo B. <rb...@gm...> - 2005-12-08 19:34:37
|
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. Do you have a file with all the rules to create in my database ? thanks, Ricardo 2005/12/8, Michael Saffitz <msa...@pc...>: > > > 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=3DHASH(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=3DHASH(0xaa904b0)', > >> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY > >> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1813 > >> GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1680 > >> GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/ > >> Plugin/InsertSequenceFeatures.pm line 731 > >> > >> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'Bio::Seq::RichSeq=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(0xaa904b0)', > >> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY > >> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1813 > >> GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1680 > >> GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/ > >> Plugin/InsertSequenceFeatures.pm line 731 > >> > >> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'Bio::Seq::RichSeq=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(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=3DHASH(0x91f4d14)', > >> > 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(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=3DHASH(0x987901c)', 'HASH(0x9889d48)') > >> > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613 > >> > GUS::ObjRelP::DbiRow::insert > >> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)') called at /GUS/ > >> > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 > >> > > >> > > >> > thanks, > >> > Ricardo > >> > >> > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep through > > log files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. DOWNLOAD > > SPLUNK! > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Michael S. <msa...@pc...> - 2005-12-08 19:39:22
|
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 |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X