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

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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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>>>>        
>>>>
>>>
>>>
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>>>      
>>>
>>    
>>