Re: [Gusdev-gusdev] LoadPfam compile error and a question

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Hey steve-
I haven't used the +create option yet, but I get an error from the
following command:
ga +create GUS::Common::Plugin::LoadPfam
(and the same error with a --commit afterward).
The error:
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/.gus.properties
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::st execute failed: ORA-01401: inserted value too large for
column (DBD ERROR: OCIStmtExecute) at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.

 SQL ERROR!! involving

    INSERT INTO Core.AlgorithmParamKey (  description, row_user_id,
algorithm_param_key, user_write, group_write, algorithm_implementation_id,
algorithm_param_key_type_id, row_project_id, group_read, row_group_id,
other_read, modification_date, user_read, row_alg_invocation_id,
algorithm_param_key_id, other_write, is_list_valued )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
 Values: Flat file containing the release of Pfam to load.  Expects
			the file containing the annotation and full
alignments in Pfam
			format of all Pfam-A families (called
"Pfam-A.full" in release 5.2)
			The specified file may be in gzip (.gz) or
compressed (.Z) format., 6, flat_file, 1, 1, 100, 0, 2, 1, 3, 1, 1, 1,
462, 0, 0 at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x857fd44)',
'^J SQL ERROR!! involving^J ^J    INSERT INTO Core.AlgorithmParamKey...')
called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x857fd44)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x84646e0)', 'ARRAY(0x8773f48)', '^J
INSERT INTO Core.AlgorithmParamKey (  description, row_user...') called at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)',
'HASH(0x8773f18)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
line 621

GUS::ObjRelP::DbiRow::insert('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677

GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmParamKey=HASH(0x873ed8c)',
undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765

GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)',
'GUS::Model::Core::AlgorithmParamKey') called at
/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746

GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684

GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmImplementation=HASH(0x86ea43c)',
undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765

GUS::Model::GusRow::submitChildrenInClass('GUS::Model::Core::Algorithm=HASH(0x86e849c)',
'GUS::Model::Core::AlgorithmImplementation') called at
/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746

GUS::Model::GusRow::submitAllChildren('GUS::Model::Core::Algorithm=HASH(0x86e849c)')
called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684

GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH(0x86e849c)')
called at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763

GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
0, 'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 411

GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::LoadPfam') called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'ARRAY(0x8105184)') called at /home/gus_home/bin/ga line 11

Is this a problem with my syntax for a +create?

Michael Luchtan
http://www.cs.uga.edu/~luchtan

On Wed, 28 May 2003, Steve Fischer wrote:

> Michael-
>
> you are getting the "can't  call method submit" error because:
>   1. you are trying to use ga +update on a plugin that hasn't yet been
> registered.  use ga +create instead
>   2. ga failed to properly detect that mistake.  i have fixed it in cvs
> so that it will now give a useful error message
>
> steve
>
> MICHAEL LUCHTAN wrote:
>
> >I figured this one out.  I didn't write the plugin, and I don't have CVS
> >write access, but someone might want to change lines like 124,125 from
> >    my $flatFile  = $self>getArgs->{'flat_file'};
> >    my $release   = $self>getArgs->{'release'};
> >to
> >    my $flatFile  = $self->getArgs->{'flat_file'};
> >    my $release   = $self->getArgs->{'release'};
> >Along with numerous other occurences of the same error in revision 1.8 of
> >LoadPfam.pm.
> >
> >Also, when I try to submit the newly built module, I get an error like so:
> >Can't call method "submit" on an undefined value at
> >/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 763.
> >
> >Can anyone help me with this?
> >
> >
> >Michael Luchtan
> >http://www.cs.uga.edu/~luchtan
> >
> >
> >On Thu, 22 May 2003, Chetna Warade wrote:
> >
> >
> >
> >>Hi all,
> >>
> >>I am getting a compiler error for LoadPfam.pm
> >>Heres a snapshot:
> >>
> >>[chetna@mango chetna]$ ga
> >>GUS::Common::Plugin::LoadPfam
> >>Reading properties from
> >>/home/gus_home/config/GUS-PluginMgr.prop
> >>
> >>ERROR: Can't use bareword ("getArgs") as a HASH ref
> >>while "strict refs" in use at
> >>/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> >>line 125.
> >>Compilation failed in require at (eval 1) line 1.
> >>
> >>
> >>--------------------------- STACK TRACE
> >>-------------------------
> >>
> >>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'Can\'t use bareword ("getArgs") as a HASH ref while
> >>"strict refs...') called at
> >>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>line 249
> >>
> >>GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'GUS::Common::Plugin::LoadPfam') called at
> >>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>line 362
> >>
> >>GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'GUS::Common::Plugin::LoadPfam') called at
> >>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>line 284
> >>
> >>GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'GUS::Common::Plugin::LoadPfam') called at
> >>/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> >>line 193
> >>
> >>GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> >>'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
> >>line 11
> >>[chetna@mango chetna]$
> >>
> >>Look forward to chain of emails!,
> >>Chetna
> >>
> >>
> >>__________________________________
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> >
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