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Re: [GUSDEV] (no subject)
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From: Chris S. <sto...@pc...> - 2008-12-10 04:17:15
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Hi Isabelle, You might try some pointers here: http://gusdb.org/wiki/index.php/How%20we%20built%20TheileriaDB.org which is for a post-gres version. John, can you help? Thanks, Chris On Dec 9, 2008, at 10:04 PM, Isabelle Phan wrote: > Hello > > I just installed GUS 3.5 from www.gusdb.org/download . I am using > Postgres and trying to load ExternalDatabase.xml as described in > http://wiki.biowebdb.org/index.php/ > Gus#GUS::Supported::Plugin::LoadGusXm > l > > It does not work (see stack trace below), apparently because of a > mismatch with the schema created during the installation. > > Where do I find a copy of ExternalDatabase.xml that is compatible with > the GUS 3.5 schema? > > Thanks, > > > Isabelle > > $> ga GUS::Supported::Plugin::LoadGusXml --filename > ../data/ExternalDatabase.xml > Tue Dec 9 18:30:22 2008 ARGS algoinvo 1 > Tue Dec 9 18:30:22 2008 ARGS comment > Tue Dec 9 18:30:22 2008 ARGS commit 0 > Tue Dec 9 18:30:22 2008 ARGS debug 0 > Tue Dec 9 18:30:22 2008 ARGS filename > ../data/ExternalDatabase.xml > Tue Dec 9 18:30:22 2008 ARGS group > Tue Dec 9 18:30:22 2008 ARGS gusconfigfile > /core/trypdb/gus-test/GUS/gus.properties > Tue Dec 9 18:30:22 2008 ARGS help > Tue Dec 9 18:30:22 2008 ARGS helpHTML > Tue Dec 9 18:30:22 2008 ARGS project > Tue Dec 9 18:30:22 2008 ARGS refresh > Tue Dec 9 18:30:22 2008 ARGS sqlVerbose 0 > Tue Dec 9 18:30:22 2008 ARGS user > Tue Dec 9 18:30:22 2008 ARGS verbose 0 > Tue Dec 9 18:30:22 2008 ARGS veryVerbose 0 > Tue Dec 9 18:30:22 2008 COMMIT commit off > Tue Dec 9 18:30:22 2008 ALGINVID 5 > > ERROR: > ERROR: attempting to access attribute 'lowercase_name' of table > ExternalDatabase, but that table does not have such an attribute > > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 729 > > GUS > ::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase > =HASH(0xf3b4530)', 'lowercase_name') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line > 88 > > GUS > ::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b > 4530)', 'lowercase_name', 'assembly') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1902 > > GUS > ::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x > f3b4530)', 'ARRAY(0xee1ce10)', 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1952 > > GUS > ::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH > (0xf0572b0)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > LoadGus > Xml.pm line 140 > > GUS > ::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa > dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > LoadGus > Xml.pm line 117 > > GUS > ::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus > Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 469 > eval {...} called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 461 > > GUS > ::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: > :GusApplication=HASH(0xe6512a0)', > 'GUS::Supported::Plugin::LoadGusXml', > 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 380 > > GUS > ::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl > ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called > at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 288 > > GUS > ::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 197 > > GUS > ::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at > /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11 > > STACK TRACE: > at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm > line 729 > > GUS > ::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase > =HASH(0xf3b4530)', 'lowercase_name') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line > 88 > > GUS > ::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b > 4530)', 'lowercase_name', 'assembly') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1902 > > GUS > ::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x > f3b4530)', 'ARRAY(0xee1ce10)', 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line > 1952 > > GUS > ::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH > (0xf0572b0)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > LoadGus > Xml.pm line 140 > > GUS > ::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa > dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > LoadGus > Xml.pm line 117 > > GUS > ::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus > Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 469 > eval {...} called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 461 > > GUS > ::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: > :GusApplication=HASH(0xe6512a0)', > 'GUS::Supported::Plugin::LoadGusXml', > 1) called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 380 > > GUS > ::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl > ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called > at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 288 > > GUS > ::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at > /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication > .pm line 197 > > GUS > ::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat > ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at > /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11 > -- > Isabelle Phan, DPhil > Seattle Biomedical Research Institute > +1(206)256 7113 > > ------------------------------------------------------------------------------ > SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, > Nevada. > The future of the web can't happen without you. Join us at MIX09 to > help > pave the way to the Next Web now. Learn more and register at > http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
