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From: Adhemar <az...@gm...> - 2011-06-07 15:12:29
|
I've ran it using commit OFF so that nothing is actually inserted into the database. We chose this plugin because it loads not only the EST sequence but also the libraries, contacts, and references. If it eventually breaks we can use GUS::Community::Plugin::Undo. But it would be nice to have the undo subroutine. Thanks, -Adhemar 2011/6/7 Deborah Pinney <pi...@pc...> > Did your previous run actually load any rows? You can check by querying > the dots.est table with row_alg_invocation_id = 122. If there are any rows, > they will have to be deleted, otherwise you will have duplicate rows. Since > use of this plugin has been discontinued in the EuPath group, we have not > yet added an undo subroutine. I will add that now and resubmit to svn. > > Debbie > > > On 6/7/2011 10:12 AM, Deborah Pinney wrote: > > The plugin did not have an undefPointerCache(). I have added it. Please > update from svn and set that step to ready. > > Debbie > > On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: > > 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 > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 > > > _______________________________________________ > Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > -- > Atc, > Rodrigo Jardim > jar...@gm... > > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking.http://p.sf.net/sfu/ephox-dev2dev > > > _______________________________________________ > Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Deborah P. <pi...@pc...> - 2011-06-07 14:41:19
|
Did your previous run actually load any rows? You can check by querying the dots.est table with row_alg_invocation_id = 122. If there are any rows, they will have to be deleted, otherwise you will have duplicate rows. Since use of this plugin has been discontinued in the EuPath group, we have not yet added an undo subroutine. I will add that now and resubmit to svn. Debbie On 6/7/2011 10:12 AM, Deborah Pinney wrote: > The plugin did not have an undefPointerCache(). I have added it. > Please update from svn and set that step to ready. > > Debbie > > On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: >> 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... >> <mailto: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 >>> <http://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 >>> >>> >>> ------------------------------------------------------------------------------ >>> Simplify data backup and recovery for your virtual environment with vRanger. >>> Installation's a snap, and flexible recovery options mean your data is safe, >>> secure and there when you need it. Discover what all the cheering's about. >>> Get your free trial download today. >>> http://p.sf.net/sfu/quest-dev2dev2 >>> >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... <mailto:Gus...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> -- >> Deborah Farin Pinney, Ph.D. >> Data Analyst >> 1428 Blockley Hall >> Computational Biology and Informatics Laboratory >> University of Pennsylvania >> Philadelphia PA 19104-6021 >> Tel: 215-573-3116 >> Fax: 215-573-3111 >> >> >> ------------------------------------------------------------------------------ >> EditLive Enterprise is the world's most technically advanced content >> authoring tool. Experience the power of Track Changes, Inline Image >> Editing and ensure content is compliant with Accessibility Checking. >> http://p.sf.net/sfu/ephox-dev2dev >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> <mailto:Gus...@li...> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> -- >> Atc, >> Rodrigo Jardim >> jar...@gm... <mailto:jar...@gm...> >> >> > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Deborah Farin Pinney, Ph.D. Data Analyst 1428 Blockley Hall Computational Biology and Informatics Laboratory University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3116 Fax: 215-573-3111 |
|
From: Steve F. <sfi...@pc...> - 2011-06-07 14:41:08
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adhemar, are you going to write a step class? do you know how to do that? steve On 6/7/2011 10:35 AM, Adhemar wrote: > We've just tested it using ga and it worked fine. > Now we're adding it to the workflow. > Thank you so much Debbie. > -Adhemar > > > 2011/6/7 Deborah Pinney <pi...@pc... > <mailto:pi...@pc...>> > > The plugin did not have an undefPointerCache(). I have added it. > Please update from svn and set that step to ready. > > Debbie > > > On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: >> 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... >> <mailto: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 >>> <http://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 >>> >>> >>> ------------------------------------------------------------------------------ >>> Simplify data backup and recovery for your virtual environment with vRanger. >>> Installation's a snap, and flexible recovery options mean your data is safe, >>> secure and there when you need it. Discover what all the cheering's about. >>> Get your free trial download today. >>> http://p.sf.net/sfu/quest-dev2dev2 >>> >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... <mailto:Gus...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> -- >> Deborah Farin Pinney, Ph.D. >> Data Analyst >> 1428 Blockley Hall >> Computational Biology and Informatics Laboratory >> University of Pennsylvania >> Philadelphia PA 19104-6021 >> Tel: 215-573-3116 >> Fax: 215-573-3111 >> >> >> ------------------------------------------------------------------------------ >> EditLive Enterprise is the world's most technically advanced >> content >> authoring tool. Experience the power of Track Changes, Inline >> Image >> Editing and ensure content is compliant with Accessibility >> Checking. >> http://p.sf.net/sfu/ephox-dev2dev >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> <mailto:Gus...@li...> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> -- >> Atc, >> Rodrigo Jardim >> jar...@gm... <mailto:jar...@gm...> >> >> > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Adhemar <az...@gm...> - 2011-06-07 14:35:28
|
We've just tested it using ga and it worked fine. Now we're adding it to the workflow. Thank you so much Debbie. -Adhemar 2011/6/7 Deborah Pinney <pi...@pc...> > The plugin did not have an undefPointerCache(). I have added it. Please > update from svn and set that step to ready. > > Debbie > > > On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: > > 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 > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 > > > _______________________________________________ > Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > -- > Atc, > Rodrigo Jardim > jar...@gm... > > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > |
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From: Deborah P. <pi...@pc...> - 2011-06-07 14:12:54
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The plugin did not have an undefPointerCache(). I have added it. Please update from svn and set that step to ready. Debbie On 6/7/2011 9:57 AM, Rodrigo Jardim wrote: > 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... > <mailto: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 >> <http://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 >> >> >> ------------------------------------------------------------------------------ >> Simplify data backup and recovery for your virtual environment with vRanger. >> Installation's a snap, and flexible recovery options mean your data is safe, >> secure and there when you need it. Discover what all the cheering's about. >> Get your free trial download today. >> http://p.sf.net/sfu/quest-dev2dev2 >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... <mailto:Gus...@li...> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > <mailto:Gus...@li...> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > -- > Atc, > Rodrigo Jardim > jar...@gm... <mailto:jar...@gm...> > > -- Deborah Farin Pinney, Ph.D. Data Analyst 1428 Blockley Hall Computational Biology and Informatics Laboratory University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3116 Fax: 215-573-3111 |
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From: Rodrigo J. <jar...@gm...> - 2011-06-07 13:57:25
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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 > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 > > > _______________________________________________ > Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > -- > Deborah Farin Pinney, Ph.D. > Data Analyst > 1428 Blockley Hall > Computational Biology and Informatics Laboratory > University of Pennsylvania > Philadelphia PA 19104-6021 > Tel: 215-573-3116 > Fax: 215-573-3111 > > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > -- Atc, Rodrigo Jardim jar...@gm... |
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From: Deborah P. <pi...@pc...> - 2011-06-07 13:29:40
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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 > <http://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 > > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. > http://p.sf.net/sfu/quest-dev2dev2 > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Deborah Farin Pinney, Ph.D. Data Analyst 1428 Blockley Hall Computational Biology and Informatics Laboratory University of Pennsylvania Philadelphia PA 19104-6021 Tel: 215-573-3116 Fax: 215-573-3111 |
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From: Adhemar <az...@gm...> - 2011-06-06 15:44:59
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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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From: Steve F. <sfi...@pc...> - 2011-05-11 15:12:02
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Konika, please refer to the mail i sent yesterday. i think that should help. steve On 5/11/2011 4:50 AM, chawla wrote: > Hi John, > > 1) I think so. > 2) yes, I am using PostgreSQL > > Konika > > > > On 10-05-2011 17:54, John Iodice wrote: >> Hi Konika, >> >> I don't know what file says "oracle" where it should say "postgres". >> What suggested that line of inquiry was that: >> >> 1. the message you cite below is from a Java compile that is >> referencing a class needed for running GUS on Oracle >> 2. you're using PostgreSQL, not Oracle (right?) >> 3. a PostgreSQL install doesn't need the Oracle libraries >> 4. files under $GUS_HOME configure GUS to use PostgreSQL or Oracle >> >> Can any of my fellow GUS users confirm (or correct) points 3 and 4? >> And suggest a place to look? >> >> One way to find candidates is the following command, provided it >> works on your system. (It does work on Linux and Macs): >> >> grep -rli oracle $GUS_HOME >> >> -- John >> >> On Tue, May 10, 2011 at 10:40 AM, chawla <ch...@bi... >> <mailto:ch...@bi...>> wrote: >> >> Hi >> There are many files in gus_home >> Could you specify , where to look , if postgres is replaced by >> oracle . >> >> I was getting this error: >> >> *[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - >> Unable to >> locate class* >> [InstallSchema] java.lang. >> ClassNotFoundException: oracle.jdbc.OracleDriver >> >> Thanks >> Konika >> >> >> >> > > > ------------------------------------------------------------------------------ > Achieve unprecedented app performance and reliability > What every C/C++ and Fortran developer should know. > Learn how Intel has extended the reach of its next-generation tools > to help boost performance applications - inlcuding clusters. > http://p.sf.net/sfu/intel-dev2devmay > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: chawla <ch...@bi...> - 2011-05-11 08:50:54
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Hi John, 1) I think so. 2) yes, I am using PostgreSQL Konika On 10-05-2011 17:54, John Iodice wrote: > Hi Konika, > > I don't know what file says "oracle" where it should say "postgres". > What suggested that line of inquiry was that: > > 1. the message you cite below is from a Java compile that is > referencing a class needed for running GUS on Oracle > 2. you're using PostgreSQL, not Oracle (right?) > 3. a PostgreSQL install doesn't need the Oracle libraries > 4. files under $GUS_HOME configure GUS to use PostgreSQL or Oracle > > Can any of my fellow GUS users confirm (or correct) points 3 and 4? > And suggest a place to look? > > One way to find candidates is the following command, provided it works > on your system. (It does work on Linux and Macs): > > grep -rli oracle $GUS_HOME > > -- John > > On Tue, May 10, 2011 at 10:40 AM, chawla <ch...@bi... > <mailto:ch...@bi...>> wrote: > > Hi > There are many files in gus_home > Could you specify , where to look , if postgres is replaced by > oracle . > > I was getting this error: > > *[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to > locate class* > [InstallSchema] java.lang. > ClassNotFoundException: oracle.jdbc.OracleDriver > > Thanks > Konika > > > > |
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From: John I. <io...@gm...> - 2011-05-10 15:54:08
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Hi Konika, I don't know what file says "oracle" where it should say "postgres". What suggested that line of inquiry was that: 1. the message you cite below is from a Java compile that is referencing a class needed for running GUS on Oracle 2. you're using PostgreSQL, not Oracle (right?) 3. a PostgreSQL install doesn't need the Oracle libraries 4. files under $GUS_HOME configure GUS to use PostgreSQL or Oracle Can any of my fellow GUS users confirm (or correct) points 3 and 4? And suggest a place to look? One way to find candidates is the following command, provided it works on your system. (It does work on Linux and Macs): grep -rli oracle $GUS_HOME -- John On Tue, May 10, 2011 at 10:40 AM, chawla <ch...@bi...> wrote: > Hi > There are many files in gus_home > Could you specify , where to look , if postgres is replaced by oracle . > > I was getting this error: > > *[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to > locate class* > [InstallSchema] java.lang. > ClassNotFoundException: oracle.jdbc.OracleDriver > > Thanks > Konika > > > > |
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From: Steve F. <sfi...@pc...> - 2011-05-10 15:47:14
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Chawla- the file gus_home/config/gus.config controls the jdbc connection. you will also need to but a postgres driver in gus_home/lib/java/db_driver steve On 5/10/2011 10:40 AM, chawla wrote: > Hi > There are many files in gus_home > Could you specify , where to look , if postgres is replaced by oracle . > > I was getting this error: > > *[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to > locate class* > [InstallSchema] java.lang. > ClassNotFoundException: oracle.jdbc.OracleDriver > > Thanks > Konika > > > > > ------------------------------------------------------------------------------ > Achieve unprecedented app performance and reliability > What every C/C++ and Fortran developer should know. > Learn how Intel has extended the reach of its next-generation tools > to help boost performance applications - inlcuding clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: chawla <ch...@bi...> - 2011-05-10 14:41:12
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Hi There are many files in gus_home Could you specify , where to look , if postgres is replaced by oracle . I was getting this error: *[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to locate class* [InstallSchema] java.lang. ClassNotFoundException: oracle.jdbc.OracleDriver Thanks Konika |
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From: Adhemar <az...@gm...> - 2011-05-09 20:15:33
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I've just updated to the newest gus.config version as Mark told and it worked fine. Thank you! -Adhemar 2011/5/9 Steve Fischer <sfi...@pc...> > too bad that we have this stuff in gus.config. seems like unneeded > configuration, as i can't think of a situation where it would be ok to vary > this. > > adhemar, is this hkspec documented anywhere that you have seen? > > steve > > > On 5/9/2011 3:00 PM, Mark Heiges wrote: > >> You have an outdated gus.config file which has lowercased hkspec >> column types. For example, >> hkspec.MODIFICATION_DATE=Date,0,0,false >> instead of the correct >> hkspec.MODIFICATION_DATE=DATE,0,0,false >> >> Start with a new gus.config from $PROJECT_HOME/install/gus.config.sample >> >> >> On May 9, 2011, at 11:26 AM, Adhemar wrote: >> >> You're right. The problem might not be related to dependencies >>> versions. >>> I've just changed it back to ant-1.6.5 and it's seems to be working >>> fine. >>> Probably the ant-nodpes wasn't installed before. >>> >>> But we are still stuck with that same error message: >>> >>> BUILD FAILED >>> /projects/schistodb30/project_home/install/build.xml:37: The >>> following error occurred while executing this line: >>> /projects/schistodb30/project_home/GUS/build.xml:16: The following >>> error occurred while executing this line: >>> /projects/schistodb30/project_home/GusSchema/build.xml:62: >>> java.lang.IllegalArgumentException: No enum const class >>> org.gusdb.dbadmin.model.Column$ColumnType.Date >>> >>> >>> Thanks, >>> -Adhemar >>> >>> >>> >>> 2011/5/9 Mark Heiges<mh...@ug...> >>> We use the ant-1.6.5 package for CentOS . You also have to install >>> the ant-nodeps package to provide tools.jar. >>> >>> I doubt the ant version is the cause of your attached error. >>> >>> -M >>> >>> Mark Heiges >>> EuPathDB Bioinformatics Resource Center >>> Center for Tropical and Emerging Global Diseases >>> Paul D. Coverdell Center, Rm 370 >>> 500 D. W. Brooks Drive >>> University of Georgia, Athens, GA 30602 >>> >>> >>> On May 9, 2011, at 10:03 AM, Adhemar wrote: >>> >>> Hi, >>> We're having problems during the schema installation and we're not >>> able to figure out what might be happening. >>> >>> I guess it might be related to the versions of GUS dependencies. >>> For instance, CentOS v5 comes with ant 1.6.5, which does not work >>> for GUS. >>> There are some warnings if one tries the latest (1.8.2), but it >>> works fine with the version 1.7.1 >>> >>> The error dump is attached and here is the documentation of what we >>> ran up to now: >>> http://writer.zoho.com/public/azneto/schistodb-documentation >>> >>> Thanks, >>> Adhemar >>> >>> >>> >>> < >>> dump >>> .txt >>> >>> ------------------------------------------------------------------------------ >>> WhatsUp Gold - Download Free Network Management Software >>> The most intuitive, comprehensive, and cost-effective network >>> management toolset available today. Delivers lowest initial >>> acquisition cost and overall TCO of any competing solution. >>> >>> http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> WhatsUp Gold - Download Free Network Management Software >>> The most intuitive, comprehensive, and cost-effective network >>> management toolset available today. Delivers lowest initial >>> acquisition cost and overall TCO of any competing solution. >>> >>> http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >> >> >> >> ------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> http://p.sf.net/sfu/whatsupgold-sd >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > |
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From: Steve F. <sfi...@pc...> - 2011-05-09 19:11:17
|
too bad that we have this stuff in gus.config. seems like unneeded configuration, as i can't think of a situation where it would be ok to vary this. adhemar, is this hkspec documented anywhere that you have seen? steve On 5/9/2011 3:00 PM, Mark Heiges wrote: > You have an outdated gus.config file which has lowercased hkspec > column types. For example, > hkspec.MODIFICATION_DATE=Date,0,0,false > instead of the correct > hkspec.MODIFICATION_DATE=DATE,0,0,false > > Start with a new gus.config from $PROJECT_HOME/install/gus.config.sample > > > On May 9, 2011, at 11:26 AM, Adhemar wrote: > >> You're right. The problem might not be related to dependencies >> versions. >> I've just changed it back to ant-1.6.5 and it's seems to be working >> fine. >> Probably the ant-nodpes wasn't installed before. >> >> But we are still stuck with that same error message: >> >> BUILD FAILED >> /projects/schistodb30/project_home/install/build.xml:37: The >> following error occurred while executing this line: >> /projects/schistodb30/project_home/GUS/build.xml:16: The following >> error occurred while executing this line: >> /projects/schistodb30/project_home/GusSchema/build.xml:62: >> java.lang.IllegalArgumentException: No enum const class >> org.gusdb.dbadmin.model.Column$ColumnType.Date >> >> >> Thanks, >> -Adhemar >> >> >> >> 2011/5/9 Mark Heiges<mh...@ug...> >> We use the ant-1.6.5 package for CentOS . You also have to install >> the ant-nodeps package to provide tools.jar. >> >> I doubt the ant version is the cause of your attached error. >> >> -M >> >> Mark Heiges >> EuPathDB Bioinformatics Resource Center >> Center for Tropical and Emerging Global Diseases >> Paul D. Coverdell Center, Rm 370 >> 500 D. W. Brooks Drive >> University of Georgia, Athens, GA 30602 >> >> >> On May 9, 2011, at 10:03 AM, Adhemar wrote: >> >> Hi, >> We're having problems during the schema installation and we're not >> able to figure out what might be happening. >> >> I guess it might be related to the versions of GUS dependencies. >> For instance, CentOS v5 comes with ant 1.6.5, which does not work >> for GUS. >> There are some warnings if one tries the latest (1.8.2), but it >> works fine with the version 1.7.1 >> >> The error dump is attached and here is the documentation of what we >> ran up to now: >> http://writer.zoho.com/public/azneto/schistodb-documentation >> >> Thanks, >> Adhemar >> >> >> >> < >> dump >> .txt >> ------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Mark H. <mh...@ug...> - 2011-05-09 19:02:27
|
You have an outdated gus.config file which has lowercased hkspec column types. For example, hkspec.MODIFICATION_DATE=Date,0,0,false instead of the correct hkspec.MODIFICATION_DATE=DATE,0,0,false Start with a new gus.config from $PROJECT_HOME/install/gus.config.sample On May 9, 2011, at 11:26 AM, Adhemar wrote: > You're right. The problem might not be related to dependencies > versions. > I've just changed it back to ant-1.6.5 and it's seems to be working > fine. > Probably the ant-nodpes wasn't installed before. > > But we are still stuck with that same error message: > > BUILD FAILED > /projects/schistodb30/project_home/install/build.xml:37: The > following error occurred while executing this line: > /projects/schistodb30/project_home/GUS/build.xml:16: The following > error occurred while executing this line: > /projects/schistodb30/project_home/GusSchema/build.xml:62: > java.lang.IllegalArgumentException: No enum const class > org.gusdb.dbadmin.model.Column$ColumnType.Date > > > Thanks, > -Adhemar > > > > 2011/5/9 Mark Heiges <mh...@ug...> > We use the ant-1.6.5 package for CentOS . You also have to install > the ant-nodeps package to provide tools.jar. > > I doubt the ant version is the cause of your attached error. > > -M > > Mark Heiges > EuPathDB Bioinformatics Resource Center > Center for Tropical and Emerging Global Diseases > Paul D. Coverdell Center, Rm 370 > 500 D. W. Brooks Drive > University of Georgia, Athens, GA 30602 > > > On May 9, 2011, at 10:03 AM, Adhemar wrote: > > Hi, > We're having problems during the schema installation and we're not > able to figure out what might be happening. > > I guess it might be related to the versions of GUS dependencies. > For instance, CentOS v5 comes with ant 1.6.5, which does not work > for GUS. > There are some warnings if one tries the latest (1.8.2), but it > works fine with the version 1.7.1 > > The error dump is attached and here is the documentation of what we > ran up to now: > http://writer.zoho.com/public/azneto/schistodb-documentation > > Thanks, > Adhemar > > > > < > dump > .txt > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Steve F. <sfi...@pc...> - 2011-05-09 17:06:35
|
Adhemar, i forwarded this to our colleague jerric and he figured out that the problem is that the db instance seems to be telling jdbc that the type "DATE" is "Date." we have to look further into it. steve On 5/9/2011 11:26 AM, Adhemar wrote: > You're right. The problem might not be related to dependencies versions. > I've just changed it back to ant-1.6.5 and it's seems to be working fine. > Probably the ant-nodpes wasn't installed before. > > But we are still stuck with that same error message: > > BUILD FAILED > /projects/schistodb30/project_home/install/build.xml:37: The following > error occurred while executing this line: > /projects/schistodb30/project_home/GUS/build.xml:16: The following > error occurred while executing this line: > /projects/schistodb30/project_home/GusSchema/build.xml:62: > java.lang.IllegalArgumentException: No enum const class > org.gusdb.dbadmin.model.Column$ColumnType.Date > > > Thanks, > -Adhemar > > > > 2011/5/9 Mark Heiges <mh...@ug... <mailto:mh...@ug...>> > > We use the ant-1.6.5 package for CentOS . You also have to install > the ant-nodeps package to provide tools.jar. > > I doubt the ant version is the cause of your attached error. > > -M > > Mark Heiges > EuPathDB Bioinformatics Resource Center > Center for Tropical and Emerging Global Diseases > Paul D. Coverdell Center, Rm 370 > 500 D. W. Brooks Drive > University of Georgia, Athens, GA 30602 > > > On May 9, 2011, at 10:03 AM, Adhemar wrote: > > Hi, > We're having problems during the schema installation and we're > not able to figure out what might be happening. > > I guess it might be related to the versions of GUS dependencies. > For instance, CentOS v5 comes with ant 1.6.5, which does not > work for GUS. > There are some warnings if one tries the latest (1.8.2), but > it works fine with the version 1.7.1 > > The error dump is attached and here is the documentation of > what we ran up to now: > http://writer.zoho.com/public/azneto/schistodb-documentation > > Thanks, > Adhemar > > > > <dump.txt>------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > <mailto:Gus...@li...> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Adhemar <az...@gm...> - 2011-05-09 15:26:35
|
You're right. The problem might not be related to dependencies versions. I've just changed it back to ant-1.6.5 and it's seems to be working fine. Probably the ant-nodpes wasn't installed before. But we are still stuck with that same error message: BUILD FAILED /projects/schistodb30/project_home/install/build.xml:37: The following error occurred while executing this line: /projects/schistodb30/project_home/GUS/build.xml:16: The following error occurred while executing this line: /projects/schistodb30/project_home/GusSchema/build.xml:62: java.lang.IllegalArgumentException: No enum const class org.gusdb.dbadmin.model.Column$ColumnType.Date Thanks, -Adhemar 2011/5/9 Mark Heiges <mh...@ug...> > We use the ant-1.6.5 package for CentOS . You also have to install the > ant-nodeps package to provide tools.jar. > > I doubt the ant version is the cause of your attached error. > > -M > > Mark Heiges > EuPathDB Bioinformatics Resource Center > Center for Tropical and Emerging Global Diseases > Paul D. Coverdell Center, Rm 370 > 500 D. W. Brooks Drive > University of Georgia, Athens, GA 30602 > > > On May 9, 2011, at 10:03 AM, Adhemar wrote: > > Hi, >> We're having problems during the schema installation and we're not able to >> figure out what might be happening. >> >> I guess it might be related to the versions of GUS dependencies. >> For instance, CentOS v5 comes with ant 1.6.5, which does not work for GUS. >> There are some warnings if one tries the latest (1.8.2), but it works fine >> with the version 1.7.1 >> >> The error dump is attached and here is the documentation of what we ran up >> to now: >> http://writer.zoho.com/public/azneto/schistodb-documentation >> >> Thanks, >> Adhemar >> >> >> >> >> <dump.txt>------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> >> http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > > > > > > |
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From: Steve F. <sfi...@pc...> - 2011-05-09 15:21:14
|
this looks like a compile error in a file in the schema installer, not to do with ant. probably to do with java version. we'll look into it. steve On 5/9/2011 11:12 AM, Mark Heiges wrote: > We use the ant-1.6.5 package for CentOS . You also have to install the > ant-nodeps package to provide tools.jar. > > I doubt the ant version is the cause of your attached error. > > -M > > Mark Heiges > EuPathDB Bioinformatics Resource Center > Center for Tropical and Emerging Global Diseases > Paul D. Coverdell Center, Rm 370 > 500 D. W. Brooks Drive > University of Georgia, Athens, GA 30602 > > On May 9, 2011, at 10:03 AM, Adhemar wrote: > >> Hi, >> We're having problems during the schema installation and we're not >> able to figure out what might be happening. >> >> I guess it might be related to the versions of GUS dependencies. >> For instance, CentOS v5 comes with ant 1.6.5, which does not work >> for GUS. >> There are some warnings if one tries the latest (1.8.2), but it >> works fine with the version 1.7.1 >> >> The error dump is attached and here is the documentation of what we >> ran up to now: >> http://writer.zoho.com/public/azneto/schistodb-documentation >> >> Thanks, >> Adhemar >> >> >> >> < >> dump >> .txt >> ------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Mark H. <mh...@ug...> - 2011-05-09 15:13:04
|
We use the ant-1.6.5 package for CentOS . You also have to install the ant-nodeps package to provide tools.jar. I doubt the ant version is the cause of your attached error. -M Mark Heiges EuPathDB Bioinformatics Resource Center Center for Tropical and Emerging Global Diseases Paul D. Coverdell Center, Rm 370 500 D. W. Brooks Drive University of Georgia, Athens, GA 30602 On May 9, 2011, at 10:03 AM, Adhemar wrote: > Hi, > We're having problems during the schema installation and we're not > able to figure out what might be happening. > > I guess it might be related to the versions of GUS dependencies. > For instance, CentOS v5 comes with ant 1.6.5, which does not work > for GUS. > There are some warnings if one tries the latest (1.8.2), but it > works fine with the version 1.7.1 > > The error dump is attached and here is the documentation of what we > ran up to now: > http://writer.zoho.com/public/azneto/schistodb-documentation > > Thanks, > Adhemar > > > > < > dump > .txt > > > ------------------------------------------------------------------------------ > WhatsUp Gold - Download Free Network Management Software > The most intuitive, comprehensive, and cost-effective network > management toolset available today. Delivers lowest initial > acquisition cost and overall TCO of any competing solution. > http://p.sf.net/sfu/whatsupgold-sd_______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Adhemar <az...@gm...> - 2011-05-09 14:03:20
|
[adhemar@bagre schistodb30]$ build GUS install -append -installDBSchema
Buildfile: /projects/schistodb30/project_home/install/build.xml
install:
[echo] proj=GUS
[echo] comp=
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/Bio
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/bin
[copy] Copying 8 files to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/CBIL/Bio
[copy] Copying 95 files to /projects/schistodb30/gus_home/lib/perl/CBIL/Bio
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/test/CBIL/Bio
[copy] Copying 4 files to /projects/schistodb30/gus_home/test/CBIL/Bio
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/data/CBIL/Bio
[copy] Copying 9 files to /projects/schistodb30/gus_home/data/CBIL/Bio
recordBuildState:
[propertyfile] Creating new property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/CSP
componentPartCopySub:
[copy] Copying 1 file to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/CBIL/CSP
[copy] Copying 11 files to /projects/schistodb30/gus_home/lib/perl/CBIL/CSP
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/java
[copy] Copying 2 files to /projects/schistodb30/gus_home/lib/java
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/doc/CBIL/CSP
[copy] Copying 10 files to /projects/schistodb30/gus_home/doc/CBIL/CSP
defaultJavaCompile:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/java/db_driver
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/java/not-deployed
[jar] Building jar: /projects/schistodb30/gus_home/lib/java/CBIL-CSP.jar
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/Util
componentPartCopySub:
[copy] Copying 11 files to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/CBIL/Util
[copy] Copying 17 files to /projects/schistodb30/gus_home/lib/perl/CBIL/Util
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/doc/CBIL/Util
[copy] Copying 1 file to /projects/schistodb30/gus_home/doc/CBIL/Util
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/Cider
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/CBIL/Cider
[copy] Copying 12 files to /projects/schistodb30/gus_home/lib/perl/CBIL/Cider
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/HQ
componentPartCopySub:
[copy] Copying 1 file to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/CBIL/HQ
[copy] Copying 4 files to /projects/schistodb30/gus_home/lib/perl/CBIL/HQ
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/TranscriptExpression
componentPartCopySub:
[copy] Copying 4 files to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/xml
[copy] Copying 3 files to /projects/schistodb30/gus_home/lib/xml
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/CBIL/TranscriptExpression
[copy] Copying 18 files to /projects/schistodb30/gus_home/lib/perl/CBIL/TranscriptExpression
[copy] Copied 4 empty directories to 1 empty directory under /projects/schistodb30/gus_home/lib/perl/CBIL/TranscriptExpression
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/R/TranscriptExpression
[copy] Copying 2 files to /projects/schistodb30/gus_home/lib/R/TranscriptExpression
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/ObjectMapper
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/CBIL/ObjectMapper
[copy] Copying 7 files to /projects/schistodb30/gus_home/lib/perl/CBIL/ObjectMapper
componentPartCopySub:
[copy] Copying 1 file to /projects/schistodb30/gus_home/config
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/doc/CBIL/ObjectMapper
[copy] Copying 1 file to /projects/schistodb30/gus_home/doc/CBIL/ObjectMapper
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing GUS/Supported
componentPartCopySub:
[copy] Copying 7 files to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/GUS/Supported
[copy] Copying 7 files to /projects/schistodb30/gus_home/lib/perl/GUS/Supported
componentPartCopySub:
[copy] Copying 16 files to /projects/schistodb30/gus_home/lib/java
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/GUS/Supported/Plugin
[copy] Copying 40 files to /projects/schistodb30/gus_home/lib/perl/GUS/Supported/Plugin
componentPartCopySub:
[copy] Copying 3 files to /projects/schistodb30/gus_home/config
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/doc/GUS/Supported
[copy] Copying 5 files to /projects/schistodb30/gus_home/doc/GUS/Supported
defaultJavaCompile:
[jar] Building jar: /projects/schistodb30/gus_home/lib/java/GUS-Supported.jar
svnInfo:
[exec] Result: 1
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing GUS/Community
componentPartCopySub:
[copy] Copying 11 files to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/sql
[copy] Copying 1 file to /projects/schistodb30/gus_home/lib/sql
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/GUS/Community
[copy] Copying 28 files to /projects/schistodb30/gus_home/lib/perl/GUS/Community
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/GUS/Community/Plugin
[copy] Copying 84 files to /projects/schistodb30/gus_home/lib/perl/GUS/Community/Plugin
componentPartCopySub:
[copy] Copying 11 files to /projects/schistodb30/gus_home/config
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/doc/GUS/Community
[copy] Copying 8 files to /projects/schistodb30/gus_home/doc/GUS/Community
svnInfo:
[exec] Result: 1
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing GUS/DBAdmin
componentPartCopySub:
[copy] Copying 11 files to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/GUS/DBAdmin
[copy] Copying 7 files to /projects/schistodb30/gus_home/lib/perl/GUS/DBAdmin
componentPartCopySub:
[copy] Copying 5 files to /projects/schistodb30/gus_home/lib/java
defaultJavaCompile:
[jar] Building jar: /projects/schistodb30/gus_home/lib/java/GUS-DBAdmin.jar
svnInfo:
[exec] Result: 1
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
copyLocal14Driver:
[echo] Installing local ojdbc14.jar from /oracle/app/oracle/jdbc/lib/ojdbc14.jar
[copy] Copying 1 file to /projects/schistodb30/gus_home/lib/java/db_driver
copyLocal5Driver:
[echo] Installing local ojdbc5.jar from /oracle/app/oracle/jdbc/lib/ojdbc5.ja
[echo] r
[copy] Copying 1 file to /projects/schistodb30/gus_home/lib/java/db_driver
defaultComponentInstall:
[echo] .
[echo] Installing GUS/GOPredict
componentPartCopySub:
[copy] Copying 3 files to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/GUS/GOPredict
[copy] Copying 20 files to /projects/schistodb30/gus_home/lib/perl/GUS/GOPredict
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/lib/perl/GUS/GOPredict/Plugin
[copy] Copying 9 files to /projects/schistodb30/gus_home/lib/perl/GUS/GOPredict/Plugin
componentPartCopySub:
[mkdir] Created dir: /projects/schistodb30/gus_home/doc/GUS/GOPredict
[copy] Copying 1 file to /projects/schistodb30/gus_home/doc/GUS/GOPredict
defaultJavaCompile:
[jar] Building jar: /projects/schistodb30/gus_home/lib/java/GUS-GOPredict.jar
svnInfo:
[exec] Result: 1
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing GusSchema/Definition
componentPartCopySub:
[copy] Copying 1 file to /projects/schistodb30/gus_home/bin
componentPartCopySub:
[copy] Copying 4 files to /projects/schistodb30/gus_home/config
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing GUS/DBAdmin
svnInfo:
[exec] Result: 1
recordBuildState:
[propertyfile] Updating property file: /projects/schistodb30/gus_home/config/.build.info
copyLocal14Driver:
[echo] Installing local ojdbc14.jar from /oracle/app/oracle/jdbc/lib/ojdbc14.jar
[copy] Copying 1 file to /projects/schistodb30/gus_home/lib/java/db_driver
copyLocal5Driver:
[echo] Installing local ojdbc5.jar from /oracle/app/oracle/jdbc/lib/ojdbc5.ja
[echo] r
[copy] Copying 1 file to /projects/schistodb30/gus_home/lib/java/db_driver
InstallSchema:
[InstallSchema] INFO [main] (InstallSchemaTask.java:73) - Reading database from /projects/schistodb30/project_home/GusSchema/Definition/config/gus_schema.xml
BUILD FAILED
/projects/schistodb30/project_home/install/build.xml:37: The following error occurred while executing this line:
/projects/schistodb30/project_home/GUS/build.xml:16: The following error occurred while executing this line:
/projects/schistodb30/project_home/GusSchema/build.xml:62: java.lang.IllegalArgumentException: No enum const class org.gusdb.dbadmin.model.Column$ColumnType.Date
Total time: 2 seconds
|
|
From: John I. <io...@gm...> - 2011-05-02 12:53:54
|
This error:
*[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to
locate class*
[InstallSchema] java.lang.
ClassNotFoundException: oracle.jdbc.OracleDriver
seems like the result of acting like an Oracle install in a postgres
environment. Is there a file under $GUS_HOME that says "oracle" where it
should say "postgresql"?
-- John
On Mon, May 2, 2011 at 7:18 AM, chawla <ch...@bi...> wrote:
> Hi
> I was using the one available on website that is GUS-3.5.0.0.tar.gz and it
> didn't had the mentioned code lines in GeneratorFunction.pm,
> so now I downloaded the current verion from the subversion directory as
> mentioned on webiste.
> it is slightly different from the previous version in the sense it required
> "gus.config" file to be present at "/home/chawla/GUS/gus_home/config"
> I remade the user and database in postgres , and copied the old gus.config
> at "/home/chawla/GUS/gus_home/config"
> and now the errors are different:
>
> Buildfile: /home/chawla/GUS/project_home/install/build.xml
>
> install:
> [echo] proj=GUS
> [echo] comp=
>
> defaultComponentInstall:
> [echo] .
> [echo] Installing CBIL/Bio
>
> recordBuildState:
> [propertyfile] Updating property file: /home/chawla/GUS/gus_home/config/.
> build.info
>
> defaultComponentInstall:
> [echo] .
> [echo] Installing CBIL/CSP
>
> recordBuildState:
> [propertyfile] Updating property file: /home/chawla/GUS/gus_home/config/.
> build.info
>
> defaultComponentInstall:
> [echo] .
> [echo] Installing CBIL/Util
> ................similar lines............................
>
> InstallSchema:
> *[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to
> locate class*
> [InstallSchema] java.lang.ClassNotFoundException: oracle.jdbc.OracleDriver
> [InstallSchema] at
> org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader.java:1400)
> [InstallSchema] at
> org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1341)
>
> ................similar lines....................
>
> BUILD FAILED
> /home/chawla/GUS/project_home/install/build.xml:37: The following error
> occurred while executing this line:
> /home/chawla/GUS/project_home/GUS/build.xml:16: The following error
> occurred while executing this line:
> /home/chawla/GUS/project_home/GusSchema/build.xml:62: Unable to locate
> class
>
> I checked build.xml line 62
> schema="${projectsDir}/GusSchema/Definition/config/gus_schema.xml"/>
> which seems to be present at the correct place.
>
> Hope you can help
> Konika
>
>
>
> On 05/02/2011 03:50 AM, Mark Heiges wrote:
>
> Hi Konika,
>
> Sorry, we assumed you were using Oracle when we sent the 'drop user'
> instructions. John is right about the syntax for postgres. Also, the
> instruction to drop the ApiDB schema was included by mistake in the earlier
> email. That schema is custom for our project so doesn't apply to you.
>
> What version of GUS are you using? The notdefyet error may be the result of
> an old bug that was fixed in 2005. The GUS-3.5.0.0.tar.gz file on the
> download site does not have the fix.
>
> Check the file GUS/ObjRelP/lib/perl/Generator/GeneratorFunctions.pm to see
> if it has this elsif statement around line 48:
>
> elsif (uc($oraType) eq "TIMESTAMP" ) {
> $newType .= "Timestamp";
> }
>
> I'm attaching a patched version GeneratorFunctions.pm.
>
> Alternatively you can checkout the most recent code from the Subversion
> repository. I have successfully installed the GUS schema in Postgres with
> that code.
> See http://www.gusdb.org/download.php .
>
> Mark Heiges
> EuPathDB Bioinformatics Resource Center
> Center for Tropical and Emerging Global Diseases
> Paul D. Coverdell Center, Rm 370
> 500 D. W. Brooks Drive
> University of Georgia, Athens, GA 30602
>
>
> On May 1, 2011, at 6:53 PM, John Iodice wrote:
>
> "drop user apidb cascade" is the Oracle syntax. I think the equivalent for
> postgres is:
>
> drop schema apidb;
>
> -- John
>
> On Sun, May 1, 2011 at 1:50 PM, chawla <ch...@bi...><ch...@bi...>wrote:
> Hi all
> I tried dropping the database and user , with what suggested by Dr Chris.
> I was confused with the names used here such as APIDB which doesn't looks
> looks like a user and thus I got the errors with these as shown below.
> but the database mygus and user gus_w was dropped successfully.
>
> After this I try to install gus again and got errors related to java. These
> are shown further below. Kindly suggest a possible solution.
>
>
> drop database mygus;
> DROP DATABASE
> postgres=# drop user APIDB cascade;
> ERROR: syntax error at or near "cascade"
> LINE 1: drop user APIDB cascade;
>
> ^
> postgres=# drop user STUDYVER cascade;
> ERROR: syntax error at or near "cascade"
> LINE 1: drop user STUDYVER cascade;
> ^
> postgres=# drop user TESS cascade;
> ERROR: syntax error at or near "cascade"
> LINE 1: drop user TESS cascade;
> ^
> postgres=# drop user TESSVER cascade;
> ERROR: syntax error at or near "cascade"
> LINE 1: drop user TESSVER cascade;
> ^
> postgres=# DROP ROLE gus_w;
> DROP ROLE
> postgres=# DROP ROLE gus_r;
> **********************************************
> build GUS install -append -installDBSchema
>
> errors:
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.SRes.ECPathway_Row
> [javac] public void setModificationDate (notdefyet value)
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/ECPathway_Row.java:83:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.SRes.ECPathway_Row
> [javac] public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AnatomyLOE_Row.java:78:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.DoTS.AnatomyLOE_Row
> [javac] public void setModificationDate (notdefyet value)
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AnatomyLOE_Row.java:83:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.DoTS.AnatomyLOE_Row
> [javac] public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/PROT/FeatureSet_Row.java:86:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.PROT.FeatureSet_Row
> [javac] public void setModificationDate (notdefyet value)
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/PROT/FeatureSet_Row.java:91:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.PROT.FeatureSet_Row
> [javac] public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
> [javac] ^
> [javac] Note: Some input files use unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [javac] 100 errors
>
> Thanks
> Konika
>
>
> On 04/28/2011 12:13 AM, gus...@li... wrote:
>
>
>
>
> ------
>
> Message: 3
> Date: Wed, 27 Apr 2011 11:38:40 -0300
> From: Rodrigo Jardim <jar...@gm...> <jar...@gm...>
> Subject: Re: [GUSDEV] Build failed - couldn't install GUS
> To: Chris Stoeckert <sto...@pc...> <sto...@pc...>
> Cc: gus...@li..., chawla <ch...@bi...><ch...@bi...>
> Message-ID: <BANLkTi=KeiJwV=d9i...@ma...><BANLkTi=KeiJwV=d9i...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Konika,
>
> I think your problem could be solved with the parameters -Xmx and -Xms in
> java (JRE). But, I don't know where you put this in the scripts of GUS.
> Maybe Dr. Chris know. I hope I have helped you. (sorry for my english!)
>
> Regards,
> Rodrigo Jardim
>
> 2011/4/27 Chris Stoeckert <sto...@pc...><sto...@pc...>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
>
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today. Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
> ------------------------------------------------------------------------------
>
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today. Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
>
> http://p.sf.net/sfu/whatsupgold-sd_______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
>
>
>
>
>
>
>
|
|
From: chawla <ch...@bi...> - 2011-05-02 11:19:09
|
Hi
I was using the one available on website that is GUS-3.5.0.0.tar.gz and
it didn't had the mentioned code lines in GeneratorFunction.pm,
so now I downloaded the current verion from the subversion directory as
mentioned on webiste.
it is slightly different from the previous version in the sense it
required "gus.config" file to be present at
"/home/chawla/GUS/gus_home/config"
I remade the user and database in postgres , and copied the old
gus.config at "/home/chawla/GUS/gus_home/config"
and now the errors are different:
Buildfile: /home/chawla/GUS/project_home/install/build.xml
install:
[echo] proj=GUS
[echo] comp=
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/Bio
recordBuildState:
[propertyfile] Updating property file:
/home/chawla/GUS/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/CSP
recordBuildState:
[propertyfile] Updating property file:
/home/chawla/GUS/gus_home/config/.build.info
defaultComponentInstall:
[echo] .
[echo] Installing CBIL/Util
................similar lines............................
InstallSchema:
_[InstallSchema] FATAL [main] (InstallSchemaTask.java:161) - Unable to
locate class_
[InstallSchema] java.lang.ClassNotFoundException: oracle.jdbc.OracleDriver
[InstallSchema] at
org.apache.tools.ant.AntClassLoader.findClassInComponents(AntClassLoader.java:1400)
[InstallSchema] at
org.apache.tools.ant.AntClassLoader.findClass(AntClassLoader.java:1341)
................similar lines....................
BUILD FAILED
/home/chawla/GUS/project_home/install/build.xml:37: The following error
occurred while executing this line:
/home/chawla/GUS/project_home/GUS/build.xml:16: The following error
occurred while executing this line:
/home/chawla/GUS/project_home/GusSchema/build.xml:62: Unable to locate class
I checked build.xml line 62
schema="${projectsDir}/GusSchema/Definition/config/gus_schema.xml"/>
which seems to be present at the correct place.
Hope you can help
Konika
On 05/02/2011 03:50 AM, Mark Heiges wrote:
> Hi Konika,
>
> Sorry, we assumed you were using Oracle when we sent the 'drop user'
> instructions. John is right about the syntax for postgres. Also, the
> instruction to drop the ApiDB schema was included by mistake in the
> earlier email. That schema is custom for our project so doesn't apply
> to you.
>
> What version of GUS are you using? The notdefyet error may be the
> result of an old bug that was fixed in 2005. The GUS-3.5.0.0.tar.gz
> file on the download site does not have the fix.
>
> Check the file GUS/ObjRelP/lib/perl/Generator/GeneratorFunctions.pm to
> see if it has this elsif statement around line 48:
>
> elsif (uc($oraType) eq "TIMESTAMP" ) {
> $newType .= "Timestamp";
> }
>
> I'm attaching a patched version GeneratorFunctions.pm.
>
> Alternatively you can checkout the most recent code from the
> Subversion repository. I have successfully installed the GUS schema in
> Postgres with that code.
> See http://www.gusdb.org/download.php .
>
> Mark Heiges
> EuPathDB Bioinformatics Resource Center
> Center for Tropical and Emerging Global Diseases
> Paul D. Coverdell Center, Rm 370
> 500 D. W. Brooks Drive
> University of Georgia, Athens, GA 30602
>
>
> On May 1, 2011, at 6:53 PM, John Iodice wrote:
>
>> "drop user apidb cascade" is the Oracle syntax. I think the
>> equivalent for postgres is:
>>
>> drop schema apidb;
>>
>> -- John
>>
>> On Sun, May 1, 2011 at 1:50 PM, chawla <ch...@bi...> wrote:
>> Hi all
>> I tried dropping the database and user , with what suggested by Dr
>> Chris.
>> I was confused with the names used here such as APIDB which doesn't
>> looks looks like a user and thus I got the errors with these as shown
>> below.
>> but the database mygus and user gus_w was dropped successfully.
>>
>> After this I try to install gus again and got errors related to java.
>> These are shown further below. Kindly suggest a possible solution.
>>
>>
>> drop database mygus;
>> DROP DATABASE
>> postgres=# drop user APIDB cascade;
>> ERROR: syntax error at or near "cascade"
>> LINE 1: drop user APIDB cascade;
>>
>> ^
>> postgres=# drop user STUDYVER cascade;
>> ERROR: syntax error at or near "cascade"
>> LINE 1: drop user STUDYVER cascade;
>> ^
>> postgres=# drop user TESS cascade;
>> ERROR: syntax error at or near "cascade"
>> LINE 1: drop user TESS cascade;
>> ^
>> postgres=# drop user TESSVER cascade;
>> ERROR: syntax error at or near "cascade"
>> LINE 1: drop user TESSVER cascade;
>> ^
>> postgres=# DROP ROLE gus_w;
>> DROP ROLE
>> postgres=# DROP ROLE gus_r;
>> **********************************************
>> build GUS install -append -installDBSchema
>>
>> errors:
>> [javac] symbol : class notdefyet
>> [javac] location: class org.gusdb.model.SRes.ECPathway_Row
>> [javac] public void setModificationDate (notdefyet value)
>> [javac] ^
>> [javac]
>> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/ECPathway_Row.java:83:
>> cannot find symbol
>> [javac] symbol : class notdefyet
>> [javac] location: class org.gusdb.model.SRes.ECPathway_Row
>> [javac] public notdefyet getModificationDate () { return
>> (notdefyet)get_Attribute("modification_date"); }
>> [javac] ^
>> [javac]
>> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AnatomyLOE_Row.java:78:
>> cannot find symbol
>> [javac] symbol : class notdefyet
>> [javac] location: class org.gusdb.model.DoTS.AnatomyLOE_Row
>> [javac] public void setModificationDate (notdefyet value)
>> [javac] ^
>> [javac]
>> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AnatomyLOE_Row.java:83:
>> cannot find symbol
>> [javac] symbol : class notdefyet
>> [javac] location: class org.gusdb.model.DoTS.AnatomyLOE_Row
>> [javac] public notdefyet getModificationDate () { return
>> (notdefyet)get_Attribute("modification_date"); }
>> [javac] ^
>> [javac]
>> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/PROT/FeatureSet_Row.java:86:
>> cannot find symbol
>> [javac] symbol : class notdefyet
>> [javac] location: class org.gusdb.model.PROT.FeatureSet_Row
>> [javac] public void setModificationDate (notdefyet value)
>> [javac] ^
>> [javac]
>> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/PROT/FeatureSet_Row.java:91:
>> cannot find symbol
>> [javac] symbol : class notdefyet
>> [javac] location: class org.gusdb.model.PROT.FeatureSet_Row
>> [javac] public notdefyet getModificationDate () { return
>> (notdefyet)get_Attribute("modification_date"); }
>> [javac] ^
>> [javac] Note: Some input files use unchecked or unsafe operations.
>> [javac] Note: Recompile with -Xlint:unchecked for details.
>> [javac] 100 errors
>>
>> Thanks
>> Konika
>>
>>
>> On 04/28/2011 12:13 AM, gus...@li...
>> wrote:
>>>
>>>
>>> ------
>>>
>>> Message: 3
>>> Date: Wed, 27 Apr 2011 11:38:40 -0300
>>> From: Rodrigo Jardim <jar...@gm...>
>>> Subject: Re: [GUSDEV] Build failed - couldn't install GUS
>>> To: Chris Stoeckert <sto...@pc...>
>>> Cc: gus...@li..., chawla <ch...@bi...>
>>> Message-ID: <BANLkTi=KeiJwV=d9i...@ma...>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Dear Konika,
>>>
>>> I think your problem could be solved with the parameters -Xmx and
>>> -Xms in
>>> java (JRE). But, I don't know where you put this in the scripts of GUS.
>>> Maybe Dr. Chris know. I hope I have helped you. (sorry for my
>>> english!)
>>>
>>> Regards,
>>> Rodrigo Jardim
>>>
>>> 2011/4/27 Chris Stoeckert <sto...@pc...>
>>>
>>>
>>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today. Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>> ------------------------------------------------------------------------------
>>
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today. Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd_______________________________________________
>>
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
>
>
>
>
|
|
From: Mark H. <mh...@ug...> - 2011-05-02 01:50:58
|
Hi Konika,
Sorry, we assumed you were using Oracle when we sent the 'drop user'
instructions. John is right about the syntax for postgres. Also, the
instruction to drop the ApiDB schema was included by mistake in the
earlier email. That schema is custom for our project so doesn't apply
to you.
What version of GUS are you using? The notdefyet error may be the
result of an old bug that was fixed in 2005. The GUS-3.5.0.0.tar.gz
file on the download site does not have the fix.
Check the file GUS/ObjRelP/lib/perl/Generator/GeneratorFunctions.pm to
see if it has this elsif statement around line 48:
elsif (uc($oraType) eq "TIMESTAMP" ) {
$newType .= "Timestamp";
}
I'm attaching a patched version GeneratorFunctions.pm.
Alternatively you can checkout the most recent code from the
Subversion repository. I have successfully installed the GUS schema in
Postgres with that code.
See http://www.gusdb.org/download.php .
Mark Heiges
EuPathDB Bioinformatics Resource Center
Center for Tropical and Emerging Global Diseases
Paul D. Coverdell Center, Rm 370
500 D. W. Brooks Drive
University of Georgia, Athens, GA 30602
|
|
From: John I. <io...@gm...> - 2011-05-01 22:53:11
|
"drop user apidb cascade" is the Oracle syntax. I think the equivalent for
postgres is:
drop schema apidb;
-- John
On Sun, May 1, 2011 at 1:50 PM, chawla <ch...@bi...> wrote:
> Hi all
> I tried dropping the database and user , with what suggested by Dr Chris.
> I was confused with the names used here such as APIDB which doesn't looks
> looks like a user and thus I got the errors with these as shown below.
> but the database mygus and user gus_w was dropped successfully.
>
> After this I try to install gus again and got errors related to java. These
> are shown further below. Kindly suggest a possible solution.
>
>
> drop database mygus;
> DROP DATABASE
> postgres=# drop user APIDB cascade;
> ERROR: syntax error at or near "cascade"
> LINE 1: drop user APIDB cascade;
>
> ^
> postgres=# drop user STUDYVER cascade;
> ERROR: syntax error at or near "cascade"
> LINE 1: drop user STUDYVER cascade;
> ^
> postgres=# drop user TESS cascade;
> ERROR: syntax error at or near "cascade"
> LINE 1: drop user TESS cascade;
> ^
> postgres=# drop user TESSVER cascade;
> ERROR: syntax error at or near "cascade"
> LINE 1: drop user TESSVER cascade;
> ^
> postgres=# DROP ROLE gus_w;
> DROP ROLE
> postgres=# DROP ROLE gus_r;
> **********************************************
> build GUS install -append -installDBSchema
>
> errors:
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.SRes.ECPathway_Row
> [javac] public void setModificationDate (notdefyet value)
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/SRes/ECPathway_Row.java:83:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.SRes.ECPathway_Row
> [javac] public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AnatomyLOE_Row.java:78:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.DoTS.AnatomyLOE_Row
> [javac] public void setModificationDate (notdefyet value)
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/DoTS/AnatomyLOE_Row.java:83:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.DoTS.AnatomyLOE_Row
> [javac] public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/PROT/FeatureSet_Row.java:86:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.PROT.FeatureSet_Row
> [javac] public void setModificationDate (notdefyet value)
> [javac] ^
> [javac]
> /home/chawla/GUS/project_home/GUS/Model/src/java/org/gusdb/model/PROT/FeatureSet_Row.java:91:
> cannot find symbol
> [javac] symbol : class notdefyet
> [javac] location: class org.gusdb.model.PROT.FeatureSet_Row
> [javac] public notdefyet getModificationDate () { return
> (notdefyet)get_Attribute("modification_date"); }
> [javac] ^
> [javac] Note: Some input files use unchecked or unsafe operations.
> [javac] Note: Recompile with -Xlint:unchecked for details.
> [javac] 100 errors
>
> Thanks
> Konika
>
>
> On 04/28/2011 12:13 AM, gus...@li... wrote:
>
>
>
> ------
>
> Message: 3
> Date: Wed, 27 Apr 2011 11:38:40 -0300
> From: Rodrigo Jardim <jar...@gm...> <jar...@gm...>
> Subject: Re: [GUSDEV] Build failed - couldn't install GUS
> To: Chris Stoeckert <sto...@pc...> <sto...@pc...>
> Cc: gus...@li..., chawla <ch...@bi...> <ch...@bi...>
> Message-ID: <BANLkTi=KeiJwV=d9i...@ma...> <BANLkTi=KeiJwV=d9i...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Konika,
>
> I think your problem could be solved with the parameters -Xmx and -Xms in
> java (JRE). But, I don't know where you put this in the scripts of GUS.
> Maybe Dr. Chris know. I hope I have helped you. (sorry for my english!)
>
> Regards,
> Rodrigo Jardim
>
> 2011/4/27 Chris Stoeckert <sto...@pc...> <sto...@pc...>
>
>
>
>
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>
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