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[Gusdev-gusdev] GUS Postgres Error
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From: <pa...@pa...> - 2004-12-10 18:19:56
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Hello all,<br />we're doing a GUS-Postgres installation from scratch here=
.
We observed all those problems that have already shown in the list and
fixed them as suggested. We're now facing some problems when loading
bootstrap data.<br /><br />When running<br
/>GUS::Common::Plugin::UpdateGusFromXML <br /><br />we got:<br /><br
/>DBD::Pg::st execute failed: ERROR:=A0 Bad numeric input format '' at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line<br />(complete
dump below)<br /><br />If we change the table structure to accept
characters instead of numeric values, we get this error:<br /><br
/>DBD::Pg::st execute failed: ERROR:=A0 value too long for type character=
(1)
at /usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147,
<GEN0> line <br />(complete dump below)<br /><br />Do you have any
thoughts on this?<br /><br />Any help would be much appreciated.<br /><br
/>Pablo N. Mendes<br />pab...@uf...<br />MSc candidate<br />Federa=
l
University of Rio de Janeiro<br /><br />##############################<br
/>[pablo@kineto1 Bootstrapping]$ ga GUS::Common::Plugin::UpdateGusFromXML
--commit --filename=3DDoTS.SequenceType.xml<br />DBD::Pg::st execute fail=
ed:
ERROR:=A0 Bad numeric input format '' at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147.<br />=A0<=
br
/>=A0SQL ERROR!! involving<br />=A0 <br />=A0=A0=A0 INSERT INTO Core.Algo=
rithmParam
(=A0 algorithm_param_key_id, group_read, user_read, other_write, order_nu=
m,
modification_date, boolean_value, row_group_id, string_value, user_write,
is_default, group_write, other_read, algorithm_param_id, row_user_id,
row_project_id, row_alg_invocation_id, algorithm_invocation_id )<br />=A0=
=A0=A0
VALUES=A0=A0 (=A0 ?, ?, ?, ?, ?, now(), '', ?, '', ?, ?, ?, ?, ?, ?, ?, ?=
, ?
)<br />=A0Values: 27, 1, 1, 0, 0, 1, 1, 0, 1, 1, 82, 5, 1, 11, 11 at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 187<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x8b9b=
990)','\x{a}
SQL ERROR!! involving\x{a} \x{a}=A0=A0=A0 INSERT INTO Core.AlgorithmParam=
...')
called at /usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
150<br />=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x8b=
9b990)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x8d1a5a4)','ARRAY(0x8d1d5c=
4)','\x{a}=A0=A0=A0
INSERT INTO Core.AlgorithmParam (=A0 algorithm_param_key_i...') called at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681<br />=A0=A0=A0=A0=
=A0=A0=A0
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmParam=3D=
HASH(0x8d1d2e8)','HASH(0x8d1d378)')
called at /usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmParam=3DHASH(0x8=
d1d2e8)')
called at /usr/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmParam=3DHASH(0x8d1=
d2e8)')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
1014<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::openInvocation('GUS::PluginMgr::GusApplic=
ation=3DHASH(0x8594c18)','GUS::Common::Plugin::UpdateGusFromXML=3DHASH(0x=
85c9380)')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
448<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x8594c18)','GUS::Common::Plugin::UpdateGusFromXML'=
,1)
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
383<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x8594c18)','GUS::Common::Plugin::UpdateGusFromXML')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
289<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x8594c18)','GUS::Common::Plugin::UpdateGusFromXML')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
198<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x8594c18)','ARRAY(0x85a84f0)')
called at /usr/gus/gus_home/bin/ga line 11<br />Database handle destroyed
without explicit disconnect.<br /><br />##########################<br
/>[pablo@kineto1 Bootstrapping]$ ga GUS::Common::Plugin::UpdateGusFromXML
--commit --filename=3DDoTS.SequenceType.xml<br />Fri Dec 10 15:24:50
2004=A0=A0=A0=A0=A0=A0=A0 COMMIT=A0 ON<br />DBD::Pg::st execute failed: E=
RROR:=A0 value too
long for type character(1) at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147,
<GEN0> line 9.<br />=A0<br />=A0SQL ERROR!! involving<br />=A0 <br =
/>=A0=A0=A0
INSERT INTO DoTS.SequenceType (=A0 group_read, sequence_type_id, user_rea=
d,
parent_sequence_type_id, other_write, modification_date, row_group_id,
user_write, hierarchy, group_write, other_read, name, description,
row_user_id, row_project_id, row_alg_invocation_id, nucleotide_type )<br
/>=A0=A0=A0 VALUES=A0=A0 (=A0 ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ?, ?, =
?, ?, ?, ?
)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0
<br />=A0Values: 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, DNA, DNA, unknown
strandedness, 5, 1, 12, DNA at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 187<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9688=
990)','\x{a}
SQL ERROR!! involving\x{a} \x{a}=A0=A0=A0 INSERT INTO DoTS.SequenceType (=
...')
called at /usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
150<br />=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x96=
88990)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x98239f8)','ARRAY(0x983a4c=
4)','\x{a}=A0=A0=A0
INSERT INTO DoTS.SequenceType (=A0 group_read, sequence_ty...') called at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681<br />=A0=A0=A0=A0=
=A0=A0=A0
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::SequenceType=3D=
HASH(0x95261a8)','HASH(0x98361bc)')
called at /usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::SequenceType=3DHASH(0x952=
61a8)')
called at /usr/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::Model::GusRow::submit('GUS::Model::DoTS::SequenceType=3DHASH(0x95261=
a8)','undef',1)
called at /usr/gus/gus_home/lib/perl/GUS/Common/Plugin/UpdateGusFromXML.p=
m
line 118<br />=A0=A0=A0=A0=A0=A0=A0
GUS::Common::Plugin::UpdateGusFromXML::process('GUS::Common::Plugin::Upda=
teGusFromXML=3DHASH(0x90b6380)','ARRAY(0x963c138)')
called at /usr/gus/gus_home/lib/perl/GUS/Common/Plugin/UpdateGusFromXML.p=
m
line 70=A0=A0=A0=A0=A0=A0=A0
GUS::Common::Plugin::UpdateGusFromXML::run('GUS::Common::Plugin::UpdateGu=
sFromXML=3DHASH(0x90b6380)','HASH(0x97cf774)')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
453<br />=A0=A0=A0=A0=A0=A0=A0 eval {...} called at
/usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x9081c18)','GUS::Common::Plugin::UpdateGusFromXML'=
,1)
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
383<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x9081c18)','GUS::Common::Plugin::UpdateGusFromXML')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
289<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x9081c18)','GUS::Common::Plugin::UpdateGusFromXML')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
198<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x9081c18)','ARRAY(0x90954f0)')
called at /usr/gus/gus_home/bin/ga line 11<br />[pablo@kineto1
Bootstrapping]$ ga GUS::Common::Plugin::UpdateGusFromXML --commit
--filename=3DDoTS.SequenceType.xml<br />Fri Dec 10 15:26:54 2004=A0=A0=A0=
=A0=A0=A0=A0
COMMIT=A0 ON<br />DBD::Pg::st execute failed: ERROR:=A0 value too long fo=
r
type character(1) at /usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.p=
m
line 147, <GEN0> line 9.<br />=A0<br />=A0SQL ERROR!! involving<br =
/>=A0
<br />=A0=A0=A0 INSERT INTO DoTS.SequenceType (=A0 group_read, sequence_t=
ype_id,
user_read, parent_sequence_type_id, other_write, modification_date,
row_group_id, user_write, hierarchy, group_write, other_read, name,
description, row_user_id, row_project_id, row_alg_invocation_id,
nucleotide_type )<br />=A0=A0=A0 VALUES=A0=A0 (=A0 ?, ?, ?, ?, ?, now(), =
?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?
)=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0
<br />=A0Values: 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, DNA, DNA, unknown
strandedness, 5, 1, 13, DNA at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 187<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9094=
990)','\x{a}
SQL ERROR!! involving\x{a} \x{a}=A0=A0=A0 INSERT INTO DoTS.SequenceType (=
...')
called at /usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
150<br />=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=3DHASH(0x90=
94990)','GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x922f9f8)','ARRAY(0x92464c=
4)','\x{a}=A0=A0=A0
INSERT INTO DoTS.SequenceType (=A0 group_read, sequence_ty...') called at
/usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681<br />=A0=A0=A0=A0=
=A0=A0=A0
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::SequenceType=3D=
HASH(0x8f321a8)','HASH(0x92421bc)')
called at /usr/gus/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::SequenceType=3DHASH(0x8f3=
21a8)')
called at /usr/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::Model::GusRow::submit('GUS::Model::DoTS::SequenceType=3DHASH(0x8f321=
a8)','undef',1)
called at /usr/gus/gus_home/lib/perl/GUS/Common/Plugin/UpdateGusFromXML.p=
m
line 118<br />=A0=A0=A0=A0=A0=A0=A0
GUS::Common::Plugin::UpdateGusFromXML::process('GUS::Common::Plugin::Upda=
teGusFromXML=3DHASH(0x8ac2380)','ARRAY(0x9048138)')
called at /usr/gus/gus_home/lib/perl/GUS/Common/Plugin/UpdateGusFromXML.p=
m
line 70=A0=A0=A0=A0=A0=A0=A0
GUS::Common::Plugin::UpdateGusFromXML::run('GUS::Common::Plugin::UpdateGu=
sFromXML=3DHASH(0x8ac2380)','HASH(0x91db774)')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
453<br />=A0=A0=A0=A0=A0=A0=A0 eval {...} called at
/usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450<br
/>=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x8a8dc18)','GUS::Common::Plugin::UpdateGusFromXML'=
,1)
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
383<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x8a8dc18)','GUS::Common::Plugin::UpdateGusFromXML')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
289<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x8a8dc18)','GUS::Common::Plugin::UpdateGusFromXML')
called at /usr/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
198<br />=A0=A0=A0=A0=A0=A0=A0
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x8a8dc18)','ARRAY(0x8aa14f0)')
called at /usr/gus/gus_home/bin/ga line 11<br /><br />
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