Menu
▾
▴
Re: [GUSDEV] Inserting Sequence Features - Problem with a big reference.
|
From: Ricardo B. <rb...@gm...> - 2005-12-08 19:34:37
|
Yes Michael, this is a 3.5 install. The file exists and the rules too, but they had not been created. I created one manually. I will file a bug and submit the sql file. Do you have a file with all the rules to create in my database ? thanks, Ricardo 2005/12/8, Michael Saffitz <msa...@pc...>: > > > Yes. Is this a 3.5 install? These rules should have been created > automatically. There should be a $GUS_HOME/config/SchemaInstall- > objects.sql file (or similar, if using the trunk) that logged all > created objects/rules in the database-- are the rules in that file? > If so, then the rule was created but incorrectly-- please file a bug > if that's the case, and make sure to submit that file. > > --Mike > > On Dec 8, 2005, at 1:53 PM, Mark S. Heiges wrote: > > > That's error looks specific for Postgres which I don't use. Someone > > else may need to help here. A quick search at google.com for > > "ERROR: cannot insert into a view" or "You need an unconditional > > ON INSERT DO INSTEAD rule" turns up several clues. > > > > -Mark > > > > Mark Heiges > > CryptoDB.org > > C210 Life Sciences Building > > Center for Tropical and Emerging Global Diseases > > University of Georgia, Athens, GA 30602 > > TEL: (706) 542-1447 FAX: (706) 542-3582 > > > > > > On Dec 8, 2005, at 6:04 AM, Ricardo Balbi wrote: > > > >> Thanks Mark, > >> > >> But now I have another error. > >> It follows below: > >> > >> [rbalbi1@crithidia bancos]$ ga > >> GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/ > >> config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt -- > >> fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer > >> "2005-12-06" --commit > >> Thu Dec 8 09:04:53 2005 ARG algoinvo 1 > >> Thu Dec 8 09:04:53 2005 ARG comment > >> Thu Dec 8 09:04:53 2005 ARG commit 1 > >> Thu Dec 8 09:04:53 2005 ARG debug 0 > >> Thu Dec 8 09:04:53 2005 ARG defaultOrganism > >> Thu Dec 8 09:04:53 2005 ARG extDbName > >> Kinetoplastida_nt > >> Thu Dec 8 09:04:53 2005 ARG extDbRlsVer 2005-12-06 > >> Thu Dec 8 09:04:53 2005 ARG fileFormat genbank > >> Thu Dec 8 09:04:53 2005 ARG gff2GroupTag > >> Thu Dec 8 09:04:53 2005 ARG group > >> Thu Dec 8 09:04:53 2005 ARG gusconfigfile /GUS/ > >> gus_home/config/gus.config > >> Thu Dec 8 09:04:53 2005 ARG handlerExternalDbs > >> Thu Dec 8 09:04:53 2005 ARG help > >> Thu Dec 8 09:04:53 2005 ARG helpHTML > >> Thu Dec 8 09:04:53 2005 ARG inputFileExtension > >> Thu Dec 8 09:04:53 2005 ARG inputFileOrDir > >> kinetoplastida_nt > >> Thu Dec 8 09:04:53 2005 ARG makeSourceids > >> Thu Dec 8 09:04:53 2005 ARG mapFile /GUS/gus_home/ > >> config/genbank2gus.xml > >> Thu Dec 8 09:04:53 2005 ARG naSequenceSubclass > >> Thu Dec 8 09:04:53 2005 ARG project > >> Thu Dec 8 09:04:53 2005 ARG seqIdColumn source_id > >> Thu Dec 8 09:04:53 2005 ARG seqSoTerm > >> Thu Dec 8 09:04:53 2005 ARG seqType > >> Thu Dec 8 09:04:53 2005 ARG soCvsVersion > >> Thu Dec 8 09:04:53 2005 ARG sqlVerbose 0 > >> Thu Dec 8 09:04:53 2005 ARG testNumber > >> Thu Dec 8 09:04:53 2005 ARG user > >> Thu Dec 8 09:04:53 2005 ARG verbose 0 > >> Thu Dec 8 09:04:53 2005 ARG veryVerbose 0 > >> Thu Dec 8 09:04:53 2005 AlgInvocationId 30 > >> Thu Dec 8 09:04:53 2005 COMMIT commit on > >> Thu Dec 8 09:04:55 2005 Processing file > >> 'kinetoplastida_nt'... > >> DBD::Pg::st execute failed: ERROR: cannot insert into a view > >> HINT: You need an unconditional ON INSERT DO INSTEAD rule. > >> > >> ERROR: > >> > >> SQL ERROR!! involving > >> > >> Values: 4 at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm > >> line 166 > >> GUS::ObjRelP::DbiDbHandle::death > >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b0)', '\x{a} SQL ERROR!! > >> involving\x{a} \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ > >> GUS/ObjRelP/DbiDbHandle.pm line 150 > >> GUS::ObjRelP::DbiDbHandle::sqlExec > >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b0)', > >> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY > >> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1813 > >> GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1680 > >> GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/ > >> Plugin/InsertSequenceFeatures.pm line 731 > >> > >> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'Bio::Seq::RichSeq=3DHASH(0xb0aa2d8)', 4, 177) called at /GUS/ > >> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > >> line 330 > >> GUS::Supported::Plugin::InsertSequenceFeatures::run > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'HASH(0xabe05b0)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/ > >> GusApplication.pm line 549 > >> eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/ > >> GusApplication.pm line 541 > >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', > >> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at / > >> GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459 > >> GUS::PluginMgr::GusApplication::doMajorMode_Run > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', > >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ > >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 > >> GUS::PluginMgr::GusApplication::doMajorMode > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', > >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ > >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 > >> GUS::PluginMgr::GusApplication::parseAndRun > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', 'ARRAY > >> (0x9c96700)') called at /GUS/gus_home/bin/ga line 11 > >> > >> STACK TRACE: > >> at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 > >> GUS::ObjRelP::DbiDbHandle::death > >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b0)', '\x{a} SQL ERROR!! > >> involving\x{a} \x{a} Values: 4') called at /GUS/gus_home/lib/perl/ > >> GUS/ObjRelP/DbiDbHandle.pm line 150 > >> GUS::ObjRelP::DbiDbHandle::sqlExec > >> ('GUS::ObjRelP::DbiDbHandle=3DHASH(0xaa904b0)', > >> 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0xb2b07b0)', 'ARRAY > >> (0xa148314)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1813 > >> GUS::Model::GusRow::version('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Model/GusRow.pm > >> line 1680 > >> GUS::Model::GusRow::submit('GUS::Model::DoTS::Source=3DHASH > >> (0xb180fe0)') called at /GUS/gus_home/lib/perl/GUS/Supported/ > >> Plugin/InsertSequenceFeatures.pm line 731 > >> > >> GUS::Supported::Plugin::InsertSequenceFeatures::processFeatureTrees > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'Bio::Seq::RichSeq=3DHASH(0xb0aa2d8)', 4, 177) called at /GUS/ > >> gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > >> line 330 > >> GUS::Supported::Plugin::InsertSequenceFeatures::run > >> ('GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x9ca3920)', > >> 'HASH(0xabe05b0)') called at /GUS/gus_home/lib/perl/GUS/PluginMgr/ > >> GusApplication.pm line 549 > >> eval {...} called at /GUS/gus_home/lib/perl/GUS/PluginMgr/ > >> GusApplication.pm line 541 > >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', > >> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at / > >> GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 459 > >> GUS::PluginMgr::GusApplication::doMajorMode_Run > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', > >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ > >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 357 > >> GUS::PluginMgr::GusApplication::doMajorMode > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', > >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /GUS/ > >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 266 > >> GUS::PluginMgr::GusApplication::parseAndRun > >> ('GUS::PluginMgr::GusApplication=3DHASH(0x9c82c20)', 'ARRAY > >> (0x9c96700)') called at /GUS/gus_home/bin/ga line 11 > >> > >> Could you help me ? > >> > >> thanks again, > >> Ricardo Balbi > >> > >> > >> > >> > >> > >> 2005/12/7, Mark S. Heiges <mh...@ug...>: One short term > >> solution is to adjust your local schema "alter table > >> SRes.Reference modify (author varchar2(4000))", or something like > >> that, and then restart the loading. > >> > >> You can also file a feature request in the GUS Schema issue tracker > >> to increase that column in a future release - https:// > >> www.cbil.upenn.edu/tracker. > >> > >> On Dec 6, 2005, at 6:48 PM, Ricardo Balbi wrote: > >> > >> > Hi, > >> > > >> > I am trying to load kinetoplastida_nt, using > >> > InsertSequenceFeatures plugin. But I am not obtaining. > >> > Kinetoplastida_nt has a register whose author field exceeds the > >> > maximum size the table sres.reference . > >> > > >> > How I must proceed to load this base? > >> > > >> > It follows below the error: > >> > > >> > [rbalbi1@crithidia bancos]$ ga > >> > GUS::Supported::Plugin::InsertSequenceFeatures --mapfile $GUS_HOME/ > >> > config/genbank2gus.xml --inputFileOrDir kinetoplastida_nt -- > >> > fileFormat genbank --extDbName "Kinetoplastida_nt" --extDbRlsVer > >> > "2005-12-06" --commit > >> > Tue Dec 6 21:32:42 2005 ARG algoinvo 1 > >> > Tue Dec 6 21:32:42 2005 ARG comment > >> > Tue Dec 6 21:32:42 2005 ARG commit 1 > >> > Tue Dec 6 21:32:42 2005 ARG debug 0 > >> > Tue Dec 6 21:32:42 2005 ARG defaultOrganism > >> > Tue Dec 6 21:32:42 2005 ARG extDbName > >> > Kinetoplastida_nt > >> > Tue Dec 6 21:32:42 2005 ARG extDbRlsVer 2005-12-06 > >> > Tue Dec 6 21:32:42 2005 ARG fileFormat genbank > >> > Tue Dec 6 21:32:42 2005 ARG gff2GroupTag > >> > Tue Dec 6 21:32:42 2005 ARG group > >> > Tue Dec 6 21:32:42 2005 ARG gusconfigfile /GUS/ > >> > gus_home/config/gus.config > >> > Tue Dec 6 21:32:42 2005 ARG handlerExternalDbs > >> > Tue Dec 6 21:32:42 2005 ARG help > >> > Tue Dec 6 21:32:42 2005 ARG helpHTML > >> > Tue Dec 6 21:32:42 2005 ARG inputFileExtension > >> > Tue Dec 6 21:32:42 2005 ARG inputFileOrDir > >> > kinetoplastida_nt > >> > Tue Dec 6 21:32:42 2005 ARG makeSourceids > >> > Tue Dec 6 21:32:42 2005 ARG mapFile /GUS/gus_home/ > >> > config/genbank2gus.xml > >> > Tue Dec 6 21:32:42 2005 ARG naSequenceSubclass > >> > Tue Dec 6 21:32:42 2005 ARG project > >> > Tue Dec 6 21:32:42 2005 ARG seqIdColumn source_id > >> > Tue Dec 6 21:32:42 2005 ARG seqSoTerm > >> > Tue Dec 6 21:32:42 2005 ARG seqType > >> > Tue Dec 6 21:32:42 2005 ARG soCvsVersion > >> > Tue Dec 6 21:32:42 2005 ARG sqlVerbose 0 > >> > Tue Dec 6 21:32:42 2005 ARG testNumber > >> > Tue Dec 6 21:32:42 2005 ARG user > >> > Tue Dec 6 21:32:42 2005 ARG verbose 0 > >> > Tue Dec 6 21:32:42 2005 ARG veryVerbose 0 > >> > Tue Dec 6 21:32:42 2005 AlgInvocationId 26 > >> > Tue Dec 6 21:32:42 2005 COMMIT commit on > >> > Tue Dec 6 21:32:44 2005 Processing file > >> 'kinetoplastida_nt'... > >> > DBD::Pg::st execute failed: ERROR: value too long for type > >> > character varying(1000) > >> > > >> > ERROR: > >> > > >> > SQL ERROR!! involving > >> > > >> > INSERT INTO SRes.Reference ( journal_or_book_name, > >> > group_write, other_read, group_read, author, user_read, > >> > row_user_id, reference_id, modification_date, other_write, > >> > row_alg_invocation_id, row_project_id, row_group_id, title, > >> > user_write ) > >> > VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, now(), ?, ?, ?, ?, ?, ? ) > >> > Values: Science 309 (5733), 409-415 (2005) PUBMED 16020725, 1, > >> > 1, 1, El-Sayed,N.M., Myler,P.J., Bartholomeu,D.C., Nilsson,D., > >> > Aggarwal,G., Tran,A.N., Ghedin,E., Worthey,E.A., Delcher,A.L., > >> > Blandin,G., Westenberger, S.J., Caler,E., Cerqueira,G.C., > >> > Branche,C., Haas,B., Anupama,A., Arner,E., Aslund,L., Attipoe,P., > >> > Bontempi,E., Bringaud,F., Burton,P., Cadag,E., Campbell,D.A., > >> > Carrington,M., Crabtree,J., Darban,H., da Silveira, J.F., de > >> > Jong,P., Edwards,K., Englund,P.T., Fazelina,G., Feldblyum,T., > >> > Ferella,M., Frasch,A.C., Gull,K., Horn,D., Hou,L., Huang,Y., > >> > Kindlund,E., Klingbeil,M., Kluge,S., Koo,H., Lacerda,D., > >> > Levin, M.J., Lorenzi,H., Louie,T., Machado,C.R., McCulloch,R., > >> > McKenna,A., Mizuno,Y., Mottram,J.C., Nelson,S., Ochaya,S., > >> > Osoegawa,K., Pai,G., Parsons,M., Pentony,M., Pettersson,U., Pop,M., > >> > Ramirez,J.L., Rinta,J., Robertson,L., Salzberg, S.L., Sanchez,D.O., > >> > Seyler,A., Sharma,R., Shetty,J., Simpson,A.J., Sisk,E., Tammi,M.T., > >> > Tarleton,R., Teixeira,S., Van Aken,S., Vogt,C., Ward,P.N., > >> > Wickstead,B., Wortman,J., White,O., Fraser,C.M., Stuart, K.D. and > >> > Andersson,B., 1, 1, 6, 0, 26, 1, 1, The genome sequence of > >> > Trypanosoma cruzi, etiologic agent of Chagas disease, 1 at /GUS/ > >> > gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 > >> > GUS::ObjRelP::DbiDbHandle::death > >> > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d14)', '\x{a} SQL ERROR!! > >> > involving\x{a} \x{a} INSERT INTO SRes.Reference ( j...') called > >> > at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 150 > >> > GUS::ObjRelP::DbiDbHandle::sqlExec > >> > ('GUS::ObjRelP::DbiDbHandle=3DHASH(0x91f4d14)', > >> > 'GUS::ObjRelP::DbiDbHandle::st=3DHASH(0x8e826cc)', 'ARRAY > >> > (0x8e82708)', '\x{a} INSERT INTO SRes.Reference > >> > ( journal_or_book_name, grou...') called at /GUS/gus_home/lib/ > >> perl/ > >> > GUS/ObjRelP/DbiRow.pm line 666 > >> > GUS::ObjRelP::DbiRow::quote_and_insert > >> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)', 'HASH(0x9889d48)') > >> > called at /GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 613 > >> > GUS::ObjRelP::DbiRow::insert > >> > ('GUS::Model::SRes::Reference=3DHASH(0x987901c)') called at /GUS/ > >> > gus_home/lib/perl/GUS/Model/GusRow.pm line 1692 > >> > > >> > > >> > thanks, > >> > Ricardo > >> > >> > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep through > > log files > > for problems? Stop! Download the new AJAX search engine that makes > > searching your log files as easy as surfing the web. DOWNLOAD > > SPLUNK! > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
