Re: [GUSDEV] ApiCommonData::Load::Plugin::InsertDbESTFiles

[Rodrigo J. <jar...@gm...>]

I had this problem in InsertBlastSimilarities.pm and I put
$self->undefPointerCache(); in a loop in insertSubjects subroutine.

Bye



2011/6/7 Deborah Pinney <pi...@pc...>

>  This plugin is not used frequently. We use a different plugin when loading
> from the dbEST mirror. In the past, we used this plugin  with the crypto EST
> file that the GA group made but have not used it recently.
>
> I have seen this error but I do not recall seeing with this plugin.
>
> I will take a look at the plugin to make sure it has an undefPointerCache
> and increase the number if it does.
>
> Debbie
>
>
>
> On 6/6/2011 11:44 AM, Adhemar wrote:
>
> Hi,
> I'm trying to load ESTs using InsertDbESTFiles.pm but it fails after a
> while informing that it's not allowed to handle more than 10000 objects at
> one time.
> There's a copy of the whole output bellow.
> How to fix this?
> Thanks,
> Adhemar
>
>
>
> ga ApiCommonData::Load::Plugin::InsertDbESTFiles --inputFile
> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est
> --extDbName SjapAnhui_EstLibrary_RSRC --extDbRlsVer 2011-06-03
> Mon Jun  6 12:32:15 2011    DSN    dbi:Oracle:host=bagre.cebio.org
> ;sid=schistodb30
> Mon Jun  6 12:32:15 2011    PLUGIN
> ApiCommonData::Load::Plugin::InsertDbESTFiles
> Mon Jun  6 12:32:15 2011    ARG    algoinvo    1
> Mon Jun  6 12:32:15 2011    ARG    comment
> Mon Jun  6 12:32:15 2011    ARG    commit    0
> Mon Jun  6 12:32:15 2011    ARG    debug    0
> Mon Jun  6 12:32:15 2011    ARG    extDbName    SjapAnhui_EstLibrary_RSRC
> Mon Jun  6 12:32:15 2011    ARG    extDbRlsVer    2011-06-03
> Mon Jun  6 12:32:15 2011    ARG    group
> Mon Jun  6 12:32:15 2011    ARG    gusconfigfile
> /storage/Data/db/SchistoDB/gusApps/gus_home/config/gus.config
> Mon Jun  6 12:32:15 2011    ARG    help
> Mon Jun  6 12:32:15 2011    ARG    helpHTML
> Mon Jun  6 12:32:15 2011    ARG    inputFile
> /storage/Data/db/SchistoDB/data/manualDelivery/SchistoDB/SjapAnhui/EST/NCBI/2011-06-03/sequence.fixed.est
> Mon Jun  6 12:32:15 2011    ARG    project
> Mon Jun  6 12:32:15 2011    ARG    restartFile
> Mon Jun  6 12:32:15 2011    ARG    sqlVerbose    0
> Mon Jun  6 12:32:15 2011    ARG    user
> Mon Jun  6 12:32:15 2011    ARG    verbose    0
> Mon Jun  6 12:32:15 2011    ARG    veryVerbose    0
> Mon Jun  6 12:32:15 2011    ARG    workflowstepid    0
> Mon Jun  6 12:32:15 2011    AlgInvocationId    122
> Mon Jun  6 12:32:15 2011    COMMIT    commit off
>
>
> ERROR MESSAGE:  You have exceeded the maximum number of allowable objects
> in memory:
>   You must use the method 'undefPointerCache()' in each loop
>     to clear the cache and allow garbage collection!!
>  If you need > 10000 objects at one time,
>    then increase the default number with the method
> 'setMaximumNumberOfObjects(<number>)' at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 483
>
> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)',
> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm
> line 28
>     GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef',
> 'HASH(0x20a0aa20)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 336
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d566110)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 212
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d566110)', 345, 62) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 159
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d57af38)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 602
>     GUS::PluginMgr::GusApplication::__ANON__() called at
> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415
>     eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm
> line 407
>     Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 632
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 502
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 388
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 297
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ARRAY(0x1b7e0b48)') called
> **** /projects/gusApps/gus_home/bin/ga on line 11
>
> STACK TRACE:
> You have exceeded the maximum number of allowable objects in memory:
>   You must use the method 'undefPointerCache()' in each loop
>     to clear the cache and allow garbage collection!!
>  If you need > 10000 objects at one time,
>    then increase the default number with the method
> 'setMaximumNumberOfObjects(<number>)' at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 483
>
> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)',
> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm
> line 28
>     GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef',
> 'HASH(0x20a0aa20)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 336
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d566110)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 212
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d566110)', 345, 62) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 159
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d57af38)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 602
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 502
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 388
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 297
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ARRAY(0x1b7e0b48)') called at
> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 306
>     Error::subs::run_clauses('HASH(0x1d57b5c8)', 'You have exceeded the
> maximum number of allowable objects in ...', undef, 'ARRAY(0x1c08c988)')
> called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 426
>     Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 632
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 502
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 388
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 297
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11
>
>
> DBD::Oracle::st execute failed: ORA-12899: value too large for column
> "CORE"."ALGORITHMINVOCATION"."RESULT" (actual: 2869, maximum: 350) (DBD
> ERROR: error possibly near <*> indicator at char 143 in '
>     UPDATE  Core.AlgorithmInvocation
>     SET
>     modification_date = SYSDATE,
>     end_time = SYSDATE,
>     row_alg_invocation_id = :p1,
>     result = :<*>p2
>     WHERE   algorithm_invocation_id = :p3') [for Statement "
>     UPDATE  Core.AlgorithmInvocation
>     SET
>     modification_date = SYSDATE,
>     end_time = SYSDATE,
>     row_alg_invocation_id = ?,
>     result = ?
>     WHERE   algorithm_invocation_id = ?" with ParamValues: :p1='122',
> :p2='You have exceeded the maximum number of allowable objects in memory:
>   You must use the method 'undefPointerCache()' in each loop
>     to clear the cache and allow garbage collection!!
>  If you need > 10000 objects at one time,
>    then increase the default number with the method
> 'setMaximumNumberOfObjects(<number>)' at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 483
>
> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)',
> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm
> line 28
>     GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef',
> 'HASH(0x20a0aa20)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 336
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d566110)...', :p3='122'] at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 147, <ESTs> line 149834.
>
>
>  SQL ERROR!! involving
>
>     UPDATE  Core.AlgorithmInvocation
>     SET
>     modification_date = SYSDATE,
>     end_time = SYSDATE,
>     row_alg_invocation_id = ?,
>     result = ?
>     WHERE   algorithm_invocation_id = ?
>  Values: 122, You have exceeded the maximum number of allowable objects in
> memory:
>   You must use the method 'undefPointerCache()' in each loop
>     to clear the cache and allow garbage collection!!
>  If you need > 10000 objects at one time,
>    then increase the default number with the method
> 'setMaximumNumberOfObjects(<number>)' at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm
> line 483
>
> GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=HASH(0x1c2c5338)',
> 'GUS::Model::DoTS::NASequenceRef=HASH(0x20a0a978)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm
> line 28
>     GUS::Model::GusRow::new('GUS::Model::DoTS::NASequenceRef',
> 'HASH(0x20a0aa20)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 336
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::getOrCreateReference('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d566110)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 212
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::processEST('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d566110)', 345, 62) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/ApiCommonData/Load/Plugin/InsertDbESTFiles.pm
> line 159
>
> ApiCommonData::Load::Plugin::InsertDbESTFiles::run('ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)',
> 'HASH(0x1d57af38)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 602
>     GUS::PluginMgr::GusApplication::__ANON__() called at
> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 415
>     eval {...} called at /usr/local/lib/perl5/site_perl/5.12.3/Error.pm
> line 407
>     Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 632
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 502
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 388
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 297
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ARRAY(0x1b7e0b48)') called, 122 at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 166
>
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)',
> '\x{a} SQL ERROR!! involving\x{a} \x{a}    UPDATE
> Core.AlgorithmInvocatio...') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 150
>
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x1cf994e0)',
> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x1d9e8db8)', 'ARRAY(0x209b7700)',
> '\x{a}    UPDATE  Core.AlgorithmInvocation\x{a}    SET
> \x{a}\x{9}modificat...') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> line 731
>
> GUS::ObjRelP::DbiRow::quote_and_update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)',
> 'HASH(0x1bc91080)', 'HASH(0x20a0a588)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> line 612
>
> GUS::ObjRelP::DbiRow::update('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)')
> called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/Model/GusRow.pm
> line 1681
>
> GUS::Model::GusRow::submit('GUS::Model::Core::AlgorithmInvocation=HASH(0x1c5d7e28)',
> 1) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 1250
>
> GUS::PluginMgr::GusApplication::closeInvocation('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles=HASH(0x1c2cacd8)', 'You have
> exceeded the maximum number of allowable objects in ...') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 623
>     GUS::PluginMgr::GusApplication::__ANON__() called at
> /usr/local/lib/perl5/site_perl/5.12.3/Error.pm line 429
>     Error::subs::try('CODE(0x1d39cdf8)', 'HASH(0x1d57b5c8)') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 632
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles', 1) called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 502
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 388
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ApiCommonData::Load::Plugin::InsertDbESTFiles') called at
> /storage/Data/db/SchistoDB/gusApps/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 297
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x1b7c1d80)',
> 'ARRAY(0x1b7e0b48)') called at /projects/gusApps/gus_home/bin/ga line 11
>
>
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>
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-- 
Atc,
Rodrigo Jardim
jar...@gm...