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

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Yep-
Good call- this fixes the problem. Changed description to 512 chars.
Thanks!

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

On Wed, 28 May 2003, Steve Fischer wrote:

> michael-
>
> not sure what is going on here.  you are calling ga +create correctly,
> and the same call worked here.
>
> the SQL error is telling you that one of the values you are inserting
> into the AlgorithmParamKey table is too big. (this table describes the
> allowed params to your plugin, and the values are taken from the easycsp
> declaration in LoadPfam.pm).
>
> i did a byte count on the description value, which is the help string
> starting with "Values: Flat file containing the release...", and it
> seems the string is about 350 bytes long.  in our instance of GUS, i
> used the describe function to see what the allowed size of the
> description field is, and it is 512 characters, which is big enough to
> hold the provided description.  maybe your instance of GUS allows only
> 256????
>
> steve
>
> SQL> describe Core.AlgorithmParamKey;
>  Name                                      Null?    Type
>  ----------------------------------------- --------
> ----------------------------
>  ALGORITHM_PARAM_KEY_ID                    NOT NULL NUMBER(5)
>  ALGORITHM_IMPLEMENTATION_ID               NOT NULL NUMBER(5)
>  ALGORITHM_PARAM_KEY                       NOT NULL VARCHAR2(60)
>  ALGORITHM_PARAM_KEY_TYPE_ID               NOT NULL NUMBER(3)
>  IS_LIST_VALUED                            NOT NULL NUMBER(1)
>  DESCRIPTION                                        VARCHAR2(512)
>  MODIFICATION_DATE                         NOT NULL DATE
>  USER_READ                                 NOT NULL NUMBER(1)
>  USER_WRITE                                NOT NULL NUMBER(1)
>  GROUP_READ                                NOT NULL NUMBER(1)
>  GROUP_WRITE                               NOT NULL NUMBER(1)
>  OTHER_READ                                NOT NULL NUMBER(1)
>  OTHER_WRITE                               NOT NULL NUMBER(1)
>  ROW_USER_ID                               NOT NULL NUMBER(12)
>  ROW_GROUP_ID                              NOT NULL NUMBER(3)
>  ROW_PROJECT_ID                            NOT NULL NUMBER(3)
>  ROW_ALG_INVOCATION_ID                     NOT NULL NUMBER(12)
>
>
>
>
> MICHAEL LUCHTAN wrote:
>
> >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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