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From: Jonathan S. <js...@pc...> - 2004-06-12 14:29:15
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Gregory: This logic is in GUS::Model::GusRow::addChild. An object may not have more than one parent from any given table/class. The child object is removed from its previous parent whenever a new parent claims (adds) it. Thus, I believe, an object that had two keys to the same parent table could not belong to both parent objects at the same time. Though I prefer my original suggestion since it is faster, this suggests another work around. Sorry for the all caps, but, I DO NOT RECOMMEND THIS! Rather than getting the children via getChildren, you could SQL query for the ids then instantiate the children directly. Cheers, Jonathan ------------------------------------------------------------------------ --- Jonathan Schug Center for Bioinformatics js...@pc... Computational Biology and Informatics Lab (215) 573-3113 voice University of Pennsylvania, (215) 573-3111 fax 1401a Blockley Hall, Philadelphia, PA 19014-6021 |
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From: Mark S. H. <mh...@ug...> - 2006-05-12 21:07:11
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try ga GUS::.... 2> errorfile (2 is the file descriptor for stderr) > From: "Kumar, Sanjeev" <San...@ng...> > Date: May 12, 2006 11:29:49 AM EDT > To: <gus...@li...> > Subject: [GUSDEV] Question Regarding: InsertSequenceFeatures > > Hi Group, > I am having a problem in trapping the errors generated by > InsertSequenceFeatures in a file. > When I am using " ga GUS::....> errorfile", it captures all other > outputs except Error string / error > description. So, it is not helpful. > Also, I tried to use parameter "--failDir", it didn't do any thing. > I am sure there must be a way, pl. guide me in finding. > > Thanks > Sanjeev > |
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From: <mro...@cs...> - 2007-08-08 22:37:13
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Hello GUS group, In am running GUS version 3.5 In November 2006 I used InsertSequenceFeatures.pm successfuly to load a complete bacteria file downloaded from NCBI. Since then NCBI published a new version of the same bacteria. To delete the data from the tables and get ready to load the new data, I ran InsertSequenceFeaturesUndo.pm also successfuly, except for: - sres.reference which still has 3 (three) records. - sres.externaldatabaserelease with 1 (one) record - sres.externaldataabase with one 1 (record) Reading the InsertSequenceFeaturesUndo.pm source code it does not mention the above tables in any of the delete methods. My question is: Should I delete the data from those tables manually or is there a new version of InsertSequenceFeaturesUndo.pm. Thanks for your help Michael Robinson Bioinformatics Research Group (Biorg) Florida International University ECS 254 Tel 786-543-3553 Miami, Florida, USA 33199 |
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From: Ed R. <ed_...@be...> - 2004-09-27 18:13:58
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Everything is parsing now, but I am still getting a SQL error so nothing is going in. Here is the SQL:
INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user_write, group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, row_group_id, other_read, na_entry_id, source_id, modification_date, user_read, row_alg_invocation_id, other_write, version, division )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, AAEE01000001, 1, 104, 0, 1, INV
As far as I can tell, it's all good except for the format of the date. Here is the full error from the error log. All 18 chromosomes return the same error:
Again, thanks for everyone's help on this.
-Ed
----
------------------ entry number 1 -----------------
SQL ERROR!! involving
INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user_write, group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, row_group_id, other_read, na_entry_id, source_id, modification_date, user_read, row_alg_invocation_id, other_write, version, division )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, AAEE01000001, 1, 104, 0, 1, INV at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', '^J SQL ERROR!! involving^J ^J INSERT INTO DoTS.NAEntry ( create...') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x9ce0958)', 'ARRAY(0x9ce0808)', '^J INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user...') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', 'HASH(0x9cc906c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', undef, 1) called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)', 'GUS::Model::DoTS::NAEntry') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 284
GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 'CBIL::Bio::GenBank::ArrayStream=HASH(0x90e130c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
eval {...} called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 'HASH(0x8d0a8f8)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 453
eval {...} called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser', 1) called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 289
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dec)') called at /var/local/GUSTest/gus_home/bin/ga line 11
Ed Robinson
255 Deerfield Rd
Bogart, GA 30622
(706)425-9181
http://www.electedrobinson.com
--Learn more about the face of your neighbor, and less about your own.
-Sargent Shriver
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From: Deborah F. P. <pi...@pc...> - 2004-09-27 19:16:08
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I think the error is actually created_rel_ver which should be a number not
a string. This seems to be the source_id. The date is OK. I'm not sure why
the parser is using the source_id as the created_rel_ver value.
-Debbie
On Mon, 27 Sep 2004, Ed Robinson wrote:
> Everything is parsing now, but I am still getting a SQL error so nothing is going in. Here is the SQL:
>
> INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user_write, group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, row_group_id, other_read, na_entry_id, source_id, modification_date, user_read, row_alg_invocation_id, other_write, version, division )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, AAEE01000001, 1, 104, 0, 1, INV
>
> As far as I can tell, it's all good except for the format of the date. Here is the full error from the error log. All 18 chromosomes return the same error:
>
> Again, thanks for everyone's help on this.
>
>
> -Ed
>
> ----
>
> ------------------ entry number 1 -----------------
>
> SQL ERROR!! involving
>
> INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user_write, group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, row_group_id, other_read, na_entry_id, source_id, modification_date, user_read, row_alg_invocation_id, other_write, version, division )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, AAEE01000001, 1, 104, 0, 1, INV at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', '^J SQL ERROR!! involving^J ^J INSERT INTO DoTS.NAEntry ( create...') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x9ce0958)', 'ARRAY(0x9ce0808)', '^J INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user...') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', 'HASH(0x9cc906c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
> GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', undef, 1) called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
> GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)', 'GUS::Model::DoTS::NAEntry') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
> GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
> GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 284
> GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 'CBIL::Bio::GenBank::ArrayStream=HASH(0x90e130c)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
> eval {...} called at /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
> GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', 'HASH(0x8d0a8f8)') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 453
> eval {...} called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser', 1) called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 289
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::GBParser') called at /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dec)') called at /var/local/GUSTest/gus_home/bin/ga line 11
>
>
> Ed Robinson
> 255 Deerfield Rd
> Bogart, GA 30622
> (706)425-9181
> http://www.electedrobinson.com
>
> --Learn more about the face of your neighbor, and less about your own.
> -Sargent Shriver
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
> Project Admins to receive an Apple iPod Mini FREE for your judgement on
> who ports your project to Linux PPC the best. Sponsored by IBM.
> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
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From: Deborah F. P. <pi...@pc...> - 2004-09-27 19:31:00
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The parser requires a value for --gbRel which should be a number, the release number issued by genbank and generally found in their README.genbank file at ftp://ftp.ncbi.nih.gov/genbank/. The parser dies otherwise. Could you have given it this source_id like designation, AAEE0100000000, as the release number? Debbie On Mon, 27 Sep 2004, Deborah F. Pinney wrote: > I think the error is actually created_rel_ver which should be a number not a > string. This seems to be the source_id. The date is OK. I'm not sure why the > parser is using the source_id as the created_rel_ver value. > > -Debbie > > On Mon, 27 Sep 2004, Ed Robinson wrote: > >> Everything is parsing now, but I am still getting a SQL error so nothing >> is going in. Here is the SQL: >> >> INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user_write, >> group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, >> row_group_id, other_read, na_entry_id, source_id, modification_date, >> user_read, row_alg_invocation_id, other_write, version, division ) >> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? >> ) >> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, >> AAEE01000001, 1, 104, 0, 1, INV >> >> As far as I can tell, it's all good except for the format of the date. >> Here is the full error from the error log. All 18 chromosomes return the >> same error: >> >> Again, thanks for everyone's help on this. >> >> >> -Ed >> >> ---- >> >> ------------------ entry number 1 ----------------- >> >> SQL ERROR!! involving >> >> INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user_write, >> group_write, created_rel_ver, na_sequence_id, row_project_id, group_read, >> row_group_id, other_read, na_entry_id, source_id, modification_date, >> user_read, row_alg_invocation_id, other_write, version, division ) >> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? >> ) >> Values: 2004-4-05 00:00:00, 1, 1, 1, AAEE0100000000, 43, 1, 1, 1, 1, 43, >> AAEE01000001, 1, 104, 0, 1, INV at >> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185 >> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', >> '^J SQL ERROR!! involving^J ^J INSERT INTO DoTS.NAEntry ( create...') >> called at /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >> line 148 >> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8ab7b78)', >> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x9ce0958)', 'ARRAY(0x9ce0808)', '^J >> INSERT INTO DoTS.NAEntry ( created_date, row_user_id, user...') called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681 >> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', >> 'HASH(0x9cc906c)') called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628 >> GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)') >> called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line >> 1677 >> GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x949ea18)', >> undef, 1) called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764 >> GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)', >> 'GUS::Model::DoTS::NAEntry') called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745 >> GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') >> called at /var/local/GUSTest/gus_home/lib/perl/GUS/Model/GusRow.pm line >> 1684 >> GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x94a084c)') >> called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line >> 284 >> GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', >> 'CBIL::Bio::GenBank::ArrayStream=HASH(0x90e130c)') called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line >> 185 >> eval {...} called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line >> 184 >> GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8106d54)', >> 'HASH(0x8d0a8f8)') called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line >> 453 >> eval {...} called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line >> 450 >> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', >> 'GUS::Common::Plugin::GBParser', 1) called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line >> 383 >> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', >> 'GUS::Common::Plugin::GBParser') called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line >> 289 >> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', >> 'GUS::Common::Plugin::GBParser') called at >> /var/local/GUSTest/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line >> 198 >> >> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', >> 'ARRAY(0x8102dec)') called at /var/local/GUSTest/gus_home/bin/ga line 11 >> >> >> Ed Robinson >> 255 Deerfield Rd >> Bogart, GA 30622 >> (706)425-9181 >> http://www.electedrobinson.com >> >> --Learn more about the face of your neighbor, and less about your own. >> -Sargent Shriver >> >> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 >> Project Admins to receive an Apple iPod Mini FREE for your judgement on >> who ports your project to Linux PPC the best. Sponsored by IBM. >> Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > ------------------------------------------------------- > This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 > Project Admins to receive an Apple iPod Mini FREE for your judgement on > who ports your project to Linux PPC the best. Sponsored by IBM. > Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Isabelle P. <isa...@sb...> - 2008-12-10 03:25:56
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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 |
|
From: Chris S. <sto...@pc...> - 2008-12-10 04:17:15
|
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 |
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From: John I. <io...@gm...> - 2008-12-10 22:20:23
|
Isabelle, The version of GUS I'm using (like yours, apparently) has no "lowercase_name" column; just "external_database_id" and "name", plus the eleven GUS housekeeping columns. I suggest you remove the lowercase_name element from the input XML. We should probably do the same with the copy on the download site. John Iodice On Tue, Dec 9, 2008 at 10:04 PM, Isabelle Phan <isa...@sb...>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 > |
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