Re: [Gusdev-gusdev] Load GOOntology error--

[MICHAEL L. <lu...@cs...>]

Hey Dave-
Seems to work!  We are commiting now.  One thing we had to do though was
to go back and comment out the ancestor hack that you mentioned before for
the new CVS checkout.  Muchos gracies for the help.

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Tue, 20 May 2003, Dave Barkan wrote:

> Hey Michael,
>
> Alright I'm pretty sure I found the problem, there was some old debugging
> code I had left in there from trying to figure out the previous problem.
> I took it out so everything should run fine.  (I think the id_file issue
> still causes a problem so this latest round wasn't a total waste of time).
>
> Just being a developer myself, and not so much dealing with how GUS is
> distributed, I'm not sure what kind of divide we're trying to keep between
> developers and users.  However, I'm sure if you encounter a problem it
> would be fine (if you are up for a challenge of going through the sometimes
> confusing plugin code) for you to try to figure it out yourself, alert
> us to it, and then we can make the change to the code.
>
> You should check out the LoadGoOntology file again from CVS and go through
> the usual steps of building/updating (outlined in a previous email).  I
> hope you have solved the update/meta problems that you encountered before?
>
> Dave
>
>
> On Tue, 20 May 2003, MICHAEL LUCHTAN wrote:
>
> > Hey Dave-
> > I haven't been running it with commit, so we don't have to worry about
> > that.  But I don't think that we've found the problem yet.  I removed the
> > --id_file that I had specified and ran the following command again:
> > [luchtan@mango luchtan]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > --id_file=/home/luchtan/GOLOG --verbose
> >
> > Unfortunately I got the same error.  Here is the output to GOLOG, followed
> > by the standard out(Please let me know if there is anything I can do to expediate the
> > sitchyation.  I'm just a little unfamiliar with the schema and kind of get
> > the feeling that ya'll want a strict divide between users and developers,
> > so I am reluctant to dive into the code):
> >
> > GOLOG:
> > Term = GO:0003673 = GO:0003673
> > Term = GO:0003674 = GO:0003674
> >
> > Stdout:
> >
> > sqlExec:
> >     UPDATE  Core.AlgorithmInvocation
> >     SET
> > 	end_time = SYSDATE,
> > 	row_alg_invocation_id = ?,
> > 	modification_date = SYSDATE
> >     WHERE   algorithm_invocation_id = ?
> >   bindValues (178, 178)
> >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> >
> >  SQL ERROR!! involving
> >
> >     INSERT INTO SRes.GORelationship (  row_user_id, other_read,
> > user_write, group_write, child_term_id, row_project_id,
> > go_relationship_id, modification_date, go_relationship_type_id, user_read,
> > row_alg_invocation_id, group_read, parent_term_id, other_write,
> > row_group_id )
> >     VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
> >  Values: 6, 1, 1, 1, 2, 4, 1, 1, 178, 1, 0, 3 at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> >
> > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af100)',
> > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GORelationship ( ...')
> > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> >
> > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af100)',
> > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8d832bc)', 'ARRAY(0x8d83340)', '^J
> > INSERT INTO SRes.GORelationship (  row_user_id, other_read,...') called at
> > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> >
> > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)',
> > 'HASH(0x8a14d7c)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > line 621
> >
> > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)')
> > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> >
> > GUS::Model::GusRow::submit('GUS::Model::SRes::GORelationship=HASH(0x8c7b54c)')
> > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > line 271
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bfa6c)',
> > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882cd70)') called at
> > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> >
> > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bfa6c)',
> > 'HASH(0x882cd40)') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > 	eval {...} called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> >
> > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> >
> > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> >
> > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> >
> >
> > Michael Luchtan
> > http://www.cs.uga.edu/~luchtan
> >
> >
> > On Mon, 19 May 2003, Dave Barkan wrote:
> >
> > > Hi Michael,
> > >
> > > I figured out the problem; it's not so much the ancestor_go_term_id issue
> > > but something else instead.  It has to do with the file you specify with
> > > the --id_file flag.  This file is where GO Terms that have been loaded are
> > > written, so if you try to load more GO Terms with the same version, the
> > > plugin reads the file to skip those that have already been loaded.
> > >
> > > The problem is, if you are just testing the plugin, and not using the
> > > --commit flag (which from your provided commands, it does not appear that
> > > you are), then these processed GO ID's are still written to the file.  The
> > > quick solution is to delete the file and run the plugin again.
> > >
> > > The plugin should really get the list of processed id's from the database
> > > rather than a file; this is an optimization that we have on our to-do list
> > > but that has not been implemented.
> > >
> > > If you have been running with the --commit flag, then the solution is not
> > > so simple as just deleting the file; I actually found another bug in the
> > > process of figuring this one out.  I will fix that regardless in the next
> > > day or two, but let me know if you have been running with --commit and
> > > then I'll let you know when it's safe to re-run.
> > >
> > > If any of the above assumptions are incorrect (for example, if you have
> > > been deleting the file all along), then let me know and I'll take another
> > > look.
> > >
> > > Dave
> > >
> > >
> > > On Fri, 16 May 2003, MICHAEL LUCHTAN wrote:
> > >
> > > > Hello-
> > > > The code needs to be changed not only on line 500, but also line 474:
> > > >     my $branchGoTerm = GUS::Model::SRes::GOTerm->new({
> > > > 	go_id  => $ancestorGoId,
> > > > 	external_database_release_id => $extDbRelId,
> > > > 	source_id => $branchRootEntry->getId(),
> > > > 	name  => $branchRootEntry->getName(), #just the name
> > > > 	definition   => $branchRootEntry->getName(),
> > > > 	minimum_level => 1,
> > > > 	maximum_level => 1,
> > > > 	number_of_levels => 1,
> > > > #	ancestor_go_term_id => $tempGusId,
> > > >
> > > > But unfortunately, this did not solve the problem.  From what I can gather
> > > > of the following log, the allowing of NULL into the ancestor_go_term_id
> > > > causes another error in GORelationship.  I imagine that this table, too,
> > > > can be modified, but wanted some feedback before going through with this.
> > > > How big a problem do you think it will cause to allow ancestor_go_term_id
> > > > in table sres.goterm to be NULL?
> > > > Here is the log:
> > > > [luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > > > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > > > --id_file=/home/luchtan/GOLOG --verbose
> > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > Reading properties from /home/luchtan/gus.properties
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > >
> > > >
> > > > prepareAndExecute:     SELECT *
> > > >       FROM Core.AlgorithmImplementation
> > > >      WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
> > > >        AND cvs_revision    = '1.11.2'
> > > >
> > > >
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > >
> > > >
> > > > prepareAndExecute: select d.name,t.name,t.is_view from Core.TableInfo t,
> > > > Core.DatabaseInfo d where d.database_id = t.database_id
> > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > >
> > > > RetrieveFromDB: select * from Core.AlgorithmImplementation where
> > > > algorithm_implementation_id = ?
> > > >   bindValues (92)
> > > >
> > > >
> > > > prepareAndExecute: select login,user_id from Core.UserInfo
> > > >
> > > >
> > > > prepareAndExecute: select name,group_id from Core.GroupInfo
> > > >
> > > >
> > > > prepareAndExecute: select name,project_id from Core.ProjectInfo
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmInvocation (  end_time, row_user_id,
> > > > user_write, group_write, cpu_time, algorithm_implementation_id,
> > > > row_project_id, algorithm_invocation_id, comment_string, group_read,
> > > > row_group_id, result, other_read, cpus_used, start_time,
> > > > modification_date, user_read, row_alg_invocation_id, other_write,
> > > > machine_id )
> > > >     VALUES   (  SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?, SYSDATE,
> > > > SYSDATE, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 92, 2, 176, 1, 3, pending, 1, 1, 1, 1, 0, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > > getRelations: select * from Core.AlgorithmParamKey where
> > > > algorithm_implementation_id = ?
> > > >   bindValues (92)
> > > >
> > > > getRelations: select * from Core.AlgorithmParamKeyType where
> > > > algorithm_param_key_type_id = ?
> > > >   bindValues (2)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
> > > > )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 1, 176, 1, 1, 3, 1, 1, 176, 1795, 345, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > > getRelations: select * from Core.AlgorithmParamKeyType where
> > > > algorithm_param_key_type_id = ?
> > > >   bindValues (0)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1796, 346, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > > getRelations: select * from Core.AlgorithmParamKeyType where
> > > > algorithm_param_key_type_id = ?
> > > >   bindValues (4)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, boolean_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1797, 357, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1798, 349, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1799, 353, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, boolean_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
> > > > )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 1, 176, 1, 1, 3, 1, 1, 176, 1800, 347, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/gusdev/gus3.0-checkouts/GO,
> > > > 3, 1, 1, 176, 1801, 356, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1802, 360, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1803, 354, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1804, 344, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1805, 359, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/luchtan/gus.properties, 3,
> > > > 1, 1, 176, 1806, 343, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, /home/luchtan/GOLOG, 3, 1, 1, 176,
> > > > 1807, 352, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, boolean_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1808, 358, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1809, 351, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id, int_value,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, '', ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?,
> > > > ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1810, 348, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1811, 350, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > group_write, is_default, order_num, row_project_id,
> > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 0, 0, 2, 176, 1, 3, 1, 1, 176, 1812, 355, 0)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Function
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Component
> > > > executing Select external_database_id from sres.externaldatabase where
> > > > name = ? GO Process
> > > > Fri May 16 01:07:22 2003	loading all .ontology files in
> > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > Fri May 16 01:07:22 2003	parsing all .ontology files in preparation
> > > > for inserting into database
> > > > Fri May 16 01:07:31 2003	parsing finished; loading ontology into
> > > > database
> > > >
> > > >
> > > > prepareAndExecute: select external_database_release_id
> > > >                from sres.externalDatabaseRelease
> > > >                where version = '2.690' and external_database_id = 92
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO SRes.ExternalDatabaseRelease (  row_user_id, other_read,
> > > > user_write, group_write, external_database_id, row_project_id,
> > > > modification_date, user_read, external_database_release_id,
> > > > row_alg_invocation_id, group_read, version, other_write, row_group_id )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?, ? )
> > > >   bindValues (6, 1, 1, 1, 92, 2, 1, 95, 176, 1, 2.690, 0, 3)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > Fri May 16 01:07:31 2003	successfully submitted new entry into
> > > > SRes.ExternalDatabaseReleaseId with primary key of 95
> > > >
> > > > Fri May 16 01:07:31 2003	making root node for function
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write,
> > > > group_write, row_project_id, name, external_database_release_id,
> > > > group_read, minimum_level, row_group_id, go_term_id, other_read,
> > > > source_id, modification_date, user_read, row_alg_invocation_id,
> > > > number_of_levels, maximum_level, other_write, definition )
> > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?,
> > > > ?, ?, ? )
> > > >   bindValues (6, GO:0003674, 1, 1, 2, molecular_function, 95, 1, 1, 3, 6,
> > > > 1, GO:0003674, 1, 176, 1, 1, 0, molecular_function)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >
> > > > prepareAndExecute: Update SRes.GOTerm Set ancestor_go_term_id = 6
> > > >                where external_database_release_id = 95
> > > >                and go_term_id = 6
> > > > Fri May 16 01:07:31 2003	loading GO Terms into SRes.GOTerm
> > > >
> > > >
> > > > prepareAndExecute: select go_relationship_type_id, name
> > > >                from sres.gorelationshiptype
> > > > Fri May 16 01:07:31 2003	loading hierarchy and synonyms into
> > > > SRes.GORelationship and SRes.GOSynonym
> > > >
> > > >
> > > > sqlExec:
> > > >     INSERT INTO SRes.GORelationship (  row_user_id, other_read,
> > > > user_write, group_write, child_term_id, row_project_id,
> > > > go_relationship_id, modification_date, go_relationship_type_id, user_read,
> > > > row_alg_invocation_id, group_read, parent_term_id, other_write,
> > > > row_group_id )
> > > >     VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
> > > >   bindValues (6, 1, 1, 1, 2, 2, 1, 1, 176, 1, 0, 3)
> > > > DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> > > > ("SRES"."GORELATIONSHIP"."PARENT_TERM_ID") (DBD ERROR: OCIStmtExecute) at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 144.
> > > >
> > > >
> > > > sqlExec:
> > > >     UPDATE  Core.AlgorithmInvocation
> > > >     SET
> > > > 	end_time = SYSDATE,
> > > > 	row_alg_invocation_id = ?,
> > > > 	modification_date = SYSDATE
> > > >     WHERE   algorithm_invocation_id = ?
> > > >   bindValues (176, 176)
> > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > >
> > > >  SQL ERROR!! involving
> > > >
> > > >     INSERT INTO SRes.GORelationship (  row_user_id, other_read,
> > > > user_write, group_write, child_term_id, row_project_id,
> > > > go_relationship_id, modification_date, go_relationship_type_id, user_read,
> > > > row_alg_invocation_id, group_read, parent_term_id, other_write,
> > > > row_group_id )
> > > >     VALUES   (  ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, '', ?, ? )
> > > >  Values: 6, 1, 1, 1, 2, 2, 1, 1, 176, 1, 0, 3 at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> > > >
> > > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af194)',
> > > > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GORelationship ( ...')
> > > > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> > > >
> > > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af194)',
> > > > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8b73214)', 'ARRAY(0x8b73298)', '^J
> > > > INSERT INTO SRes.GORelationship (  row_user_id, other_read,...') called at
> > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> > > >
> > > > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)',
> > > > 'HASH(0x896950c)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > > > line 621
> > > >
> > > > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)')
> > > > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> > > >
> > > > GUS::Model::GusRow::submit('GUS::Model::SRes::GORelationship=HASH(0x8c99f84)')
> > > > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > > > line 271
> > > >
> > > > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ceb4)') called at
> > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> > > >
> > > > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > 'HASH(0x882ce84)') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > > > 	eval {...} called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> > > >
> > > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> > > >
> > > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> > > >
> > > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> > > >
> > > >
> > > > Thanks,
> > > >
> > > > Michael Luchtan
> > > > http://www.cs.uga.edu/~luchtan
> > > >
> > > >
> > > > On Fri, 16 May 2003, Dave Barkan wrote:
> > > >
> > > > > Hi Michael and folks,
> > > > >
> > > > > This is the result of a known bug in the database schema.  Right now,
> > > > > there is a non-nullable foreign key in SRes.GoTerm that points back to
> > > > > SRes.GoTerm itself (the foreign key being ancestor_go_term).
> > > > >
> > > > > I believe I submitted a request for a schema change, but until that change
> > > > > is implemented the temporary solution is a hack; when loading the root
> > > > > term of the GO Ontology, I just set the ancestor_go_term to 1, so that it
> > > > > temporarily points to whatever entry is in SRes.GoTerm with an ID of 1.
> > > > > Then I immediately update the root entry to (correctly) point to itself as
> > > > > the ancestor_go_term.
> > > > >
> > > > > However, since you are loading the Ontology for the first time, you
> > > > > obviously won't have any entry with an ID of 1; that is the cause of the
> > > > > error message you are getting.
> > > > >
> > > > > I think the only solution to this is to make the column ancestor_go_term
> > > > > nullable.  After that, you will have to take out the line in the plugin
> > > > > that does that does the hack of setting the ancestor_go_term to 1, which
> > > > > is shown here:
> > > > >
> > > > > (line 500 of LoadGoOntology.pm):
> > > > >
> > > > >  my $ontologyGoTerm = GUS::Model::SRes::GOTerm->new({
> > > > > 	go_id  => $rootGoId,
> > > > > 	external_database_release_id => $extDbRelId,
> > > > > 	source_id => $rootEntry->getId(),
> > > > > 	name  => $rootEntry->getName(), #just the name
> > > > > 	definition   => $rootEntry->getName(),
> > > > > 	minimum_level => 0,
> > > > > 	maximum_level => 0,
> > > > > 	number_of_levels => 1,
> > > > > 	ancestor_go_term_id => $tempAncestorId,  #remove this line
> > > > >     } );
> > > > >
> > > > > After reading some of the previous email traffic on the gus-dev list, I'm
> > > > > not sure if you have permissions to make these modifications.  I can make
> > > > > them for you and resubmit them to cvs, but I am hesitant to make this
> > > > > change permanent until we have the schema change to make the column
> > > > > non-nullable instituted in our copy of GUS.  This brings up some of the
> > > > > larger questions about how schema changes to GUS are ensured to remain
> > > > > consistent among all copies of GUS. I'm sure there's a protocol; while I'm
> > > > > not familiar with it I'm sure other people on this list are and could
> > > > > help you out implementing all of this.
> > > > >
> > > > > Glad you got the plugin running; did you end up passing in the external
> > > > > database ids as command line parameters or did you figure out what was
> > > > > causing the previous problem some other way?
> > > > >
> > > > > Dave
> > > > >
> > > > >
> > > > >
> > > > > On Fri, 16 May 2003, MICHAEL LUCHTAN wrote:
> > > > >
> > > > > > Dave-
> > > > > > Check it out:
> > > > > > [luchtan@mango install]$ ga GUS::GOPredict::Plugin::LoadGoOntology
> > > > > > --create_release --file_path=/home/gusdev/gus3.0-checkouts/GO
> > > > > > --id_file=/home/luchtan/GOLOG --verbose
> > > > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > > > Reading properties from /home/luchtan/gus.properties
> > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > >
> > > > >
> > > > > > executing Select external_database_id from sres.externaldatabase where
> > > > > > name = ? GO Function
> > > > > > executing Select external_database_id from sres.externaldatabase where
> > > > > > name = ? GO Component
> > > > > > executing Select external_database_id from sres.externaldatabase where
> > > > > > name = ? GO Process
> > > > > > Thu May 15 23:59:40 2003	loading all .ontology files in
> > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > Thu May 15 23:59:40 2003	parsing all .ontology files in preparation
> > > > > > for inserting into database
> > > > > > Thu May 15 23:59:49 2003	parsing finished; loading ontology into
> > > > > > database
> > > > > >
> > > > > >
> > > > > > prepareAndExecute: select external_database_release_id
> > > > > >                from sres.externalDatabaseRelease
> > > > > >                where version = '2.690' and external_database_id = 92
> > > > > >
> > > > >
> > > > > > GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology)
> > > > > > DBD::Oracle::st execute failed: ORA-02291: integrity constraint
> > > > > > (SRES.GOTERM_FK02) violated - parent key not found (DBD ERROR:
> > > > > > OCIStmtExecute) at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line
> > > > > > 144.
> > > > > >
> > > > > >
> > > > > > sqlExec:
> > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > >     SET
> > > > > > 	end_time = SYSDATE,
> > > > > > 	row_alg_invocation_id = ?,
> > > > > > 	modification_date = SYSDATE
> > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > >   bindValues (174, 174)
> > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > >
> > > > > >  SQL ERROR!! involving
> > > > > >
> > > > > >     INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write,
> > > > > > group_write, ancestor_go_term_id, row_project_id, name,
> > > > > > external_database_release_id, group_read, minimum_level, row_group_id,
> > > > > > go_term_id, other_read, source_id, modification_date, user_read,
> > > > > > row_alg_invocation_id, number_of_levels, maximum_level, other_write,
> > > > > > definition )
> > > > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?,
> > > > > > ?, ?, ?, ? )
> > > > > >  Values: 6, GO:0003673, 1, 1, 1, 2, Gene_Ontology, 93, 1, 0, 3, 3, 1,
> > > > > > GO:0003673, 1, 174, 1, 0, 0, Gene_Ontology at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
> > > > > >
> > > > > > GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> > > > > > '^J SQL ERROR!! involving^J ^J    INSERT INTO SRes.GOTerm (  row_use...')
> > > > > > called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
> > > > > >
> > > > > > GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x86af264)',
> > > > > > 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8bc753c)', 'ARRAY(0x8bc75c0)', '^J
> > > > > > INSERT INTO SRes.GOTerm (  row_user_id, go_id, user_write, ...') called at
> > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
> > > > > >
> > > > > > GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)',
> > > > > > 'HASH(0x890dc40)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> > > > > > line 621
> > > > > >
> > > > > > GUS::ObjRelP::DbiRow::insert('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> > > > > > called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
> > > > > >
> > > > > > GUS::Model::GusRow::submit('GUS::Model::SRes::GOTerm=HASH(0x890e1e0)')
> > > > > > called at /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm
> > > > > > line 512
> > > > > >
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology::__makeOntologyRoot('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > > > 'HASH(0x8e7c514)', 'GO:0003673', 93) called at
> > > > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 437
> > > > > >
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology::__makeRoots('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > > > 'HASH(0x8e7c514)', 'CBIL::Bio::GeneOntologyParser::Store=HASH(0x8b26f04)',
> > > > > > 93, undef, 'FileHandle=GLOB(0x88c801c)') called at
> > > > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 195
> > > > > >
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology::__load_ontology('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > > > 'CBIL::Bio::GeneOntologyParser::Parser=HASH(0x882ce64)') called at
> > > > > > /home/gus_home/lib/perl/GUS/GOPredict/Plugin/LoadGoOntology.pm line 144
> > > > > >
> > > > > > GUS::GOPredict::Plugin::LoadGoOntology::run('GUS::GOPredict::Plugin::LoadGoOntology=HASH(0x84bf9b8)',
> > > > > > 'HASH(0x882ce34)') called at
> > > > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 389
> > > > > > 	eval {...} called at
> > > > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385
> > > > > >
> > > > > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284
> > > > > >
> > > > > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > > > 'GUS::GOPredict::Plugin::LoadGoOntology') called at
> > > > > > /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193
> > > > > >
> > > > > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> > > > > > 'ARRAY(0x8105130)') called at /home/gus_home/bin/ga line 11
> > > > > >
> > > > > >
> > > > > > Looks like an sql error, but I'm not sure what to do about it.  Do any of
> > > > > > the rror messages give you any leads?
> > > > > >
> > > > > >
> > > > > > Michael Luchtan
> > > > > > http://www.cs.uga.edu/~luchtan
> > > > > >
> > > > > >
> > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > >
> > > > > > > Hey Michael,
> > > > > > >
> > > > > > > I still think that the error is an sql error.  It does say
> > > > > > >
> > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > >
> > > > > > > but my experience is that that message is printed out when the sql
> > > > > > > statement is not what it expects.  The fact that it also says
> > > > > > >
> > > > > > >  prepareAndExecute: select external_database_release_id
> > > > > > > >                from sres.externalDatabaseRelease
> > > > > > > >                where version = '2.690' and external_database_id =
> > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > >
> > > > > > > and doesn't print out the external_database_id in the statement is why I
> > > > > > > am focusing on the external database issue.  Here's what I did so we can
> > > > > > > narrow it down:
> > > > > > >
> > > > > > > 1.  I added an error statement if the plugin tries to run this query and
> > > > > > > can't find the database id; that way we can be sure about the problem.
> > > > > > >
> > > > > > > 2.  I added three command line arguments: function_db_id, process_db_id,
> > > > > > > and component_db_id.  You can pass these in to specify the external
> > > > > > > database ids of the respective branches, thus avoiding the
> > > > > > > programming hack of hardcoded entries in the database.
> > > > > > >
> > > > > > > To rerun, just do the following:
> > > > > > >
> > > > > > > 1. cvs update LoadGoOntology to get the version I just committed.
> > > > > > > 2. run 'build GUS/GOPredict install -append' to build the plugin.
> > > > > > > 3. run the command 'ga +update GUS::GOPredict::Plugin::LoadGoOntology
> > > > > > > --commit'
> > > > > > >
> > > > > > > (this sequence of commands generally has to be done whenever changes have
> > > > > > > been made to a plugin, especially those to the command line arguments).
> > > > > > >
> > > > > > > Try that, run it with the --verbose flag set, and let me know what you
> > > > > > > see.
> > > > > > >
> > > > > > > Dave
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > > > >
> > > > > > > > Dave-
> > > > > > > >
> > > > > > > > Yes, we ran the provided queries, and they are in the table.  Also, those
> > > > > > > > files are there as downloaded from the ftp site that you provided.
> > > > > > > > Again, here is a snapshot of where it failed(which seems more like a
> > > > > > > > compiler error than an sql error):
> > > > > > > >
> > > > > > > > sqlExec:
> > > > > > > >     INSERT INTO Core.AlgorithmParam (  row_user_id, user_write,
> > > > > > > > group_write, is_default, order_num, row_project_id,
> > > > > > > > algorithm_invocation_id, group_read, string_value, row_group_id,
> > > > > > > > other_read, modification_date, user_read, row_alg_invocation_id,
> > > > > > > > algorithm_param_id, algorithm_param_key_id, other_write )
> > > > > > > >     VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> > > > > > > >   bindValues (6, 1, 1, 0, 0, 2, 169, 1, 3, 1, 1, 169, 1740, 304, 0)
> > > > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > > > Thu May 15 03:01:35 2003	loading all .ontology files in
> > > > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > > > Thu May 15 03:01:35 2003	parsing all .ontology files in preparation
> > > > > > > > for inserting into database
> > > > > > > > Thu May 15 03:01:43 2003	parsing finished; loading ontology into
> > > > > > > > database
> > > > > > > >
> > > > > > > >
> > > > > > > > prepareAndExecute: select external_database_release_id
> > > > > > > >                from sres.externalDatabaseRelease
> > > > > > > >                where version = '2.690' and external_database_id =
> > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > prepareAndExecute FAILED:
> > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2074)->errstr
> > > > > > > >
> > > > > > > >
> > > > > > > > sqlExec:
> > > > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > > > >     SET
> > > > > > > > 	end_time = SYSDATE,
> > > > > > > > 	row_alg_invocation_id = ?,
> > > > > > > > 	modification_date = SYSDATE
> > > > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > > > >   bindValues (169, 169)
> > > > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > >
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > >
> > > > > > > > Michael Luchtan
> > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > >
> > > > > > > >
> > > > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > > > >
> > > > > > > > > Hey Michael,
> > > > > > > > >
> > > > > > > > > Alright, I'm still not sure it isn't an issue with an external database
> > > > > > > > > entry.  Try these two things.
> > > > > > > > >
> > > > > > > > > 1.Run the query 'select external_database_id from sres.externaldatabase
> > > > > > > > > where name = ?'
> > > > > > > > >
> > > > > > > > > and substitute 'GO Function,' GO Process,' 'GO Component' for each ?.
> > > > > > > > >
> > > > > > > > > 2. Make sure that the ontology files you are loading from are of the form
> > > > > > > > > 'branch.ontology' where branch can be one of 'process', 'function', or
> > > > > > > > > 'component.' These are the names of the files when they are downloaded
> > > > > > > > > from the GO site.
> > > > > > > > >
> > > > > > > > > The reason I want you to give the query a shot is that the plugin runs the
> > > > > > > > > same query to get the id's of those databases.  Then it turns around and
> > > > > > > > > uses those ids in the query that is failing:
> > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > prepareAndExecute: select external_database_release_id
> > > > > > > > > >                from sres.externalDatabaseRelease
> > > > > > > > > >                where version = '2.690' and external_database_id =
> > > > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > > >
> > > > > > > > > Sorry if this is overkill to try to figure this one out but I guess that's
> > > > > > > > > the disadvantage of debugging across state lines!
> > > > > > > > >
> > > > > > > > > dave
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > > > prepareAndExecute FAILED:
> > > > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2084)->errstr
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > sqlExec:
> > > > > > > > > >     UPDATE  Core.AlgorithmInvocation
> > > > > > > > > >     SET
> > > > > > > > > > 	end_time = SYSDATE,
> > > > > > > > > > 	row_alg_invocation_id = ?,
> > > > > > > > > > 	modification_date = SYSDATE
> > > > > > > > > >     WHERE   algorithm_invocation_id = ?
> > > > > > > > > >   bindValues (167, 167)
> > > > > > > > > >  DbiHandle:sqlExec:insert succeeded 1 row(s)
> > > > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Michael Luchtan
> > > > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Thu, 15 May 2003, Dave Barkan wrote:
> > > > > > > > > >
> > > > > > > > > > > Hey Michael,
> > > > > > > > > > >
> > > > > > > > > > > Can you run it again with the --verbose flag set, and resend the output?
> > > > > > > > > > > That will probably help me figure out the error much easier.  Thanks,
> > > > > > > > > > >
> > > > > > > > > > > Dave
> > > > > > > > > > >
> > > > > > > > > > > On Thu, 15 May 2003, MICHAEL LUCHTAN wrote:
> > > > > > > > > > >
> > > > > > > > > > > > Hello Dave-
> > > > > > > > > > > > Here is the error:
> > > > > > > > > > > >
> > > > > > > > > > > > [luchtan@mango gbparserFailures]$ ga
> > > > > > > > > > > > GUS::GOPredict::Plugin::LoadGoOntology --create_release
> > > > > > > > > > > > --file_path=/home/gusdev/gus3.0-checkouts/GO --id_file=/home/luchtan/GOLOG
> > > > > > > > > > > >
> > > > > > > > > > > > Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
> > > > > > > > > > > > Reading properties from /home/luchtan/gus.properties
> > > > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > > > DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
> > > > > > > > > > > > in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
> > > > > > > > > > > > Thu May 15 00:48:36 2003	loading all .ontology files in
> > > > > > > > > > > > /home/gusdev/gus3.0-checkouts/GO in preparation for parsing
> > > > > > > > > > > > Thu May 15 00:48:36 2003	parsing all .ontology files in preparation
> > > > > > > > > > > > for inserting into database
> > > > > > > > > > > > Thu May 15 00:48:44 2003	parsing finished; loading ontology into
> > > > > > > > > > > > database
> > > > > > > > > > > > DBD::Oracle::db prepare failed: ORA-00921: unexpected end of SQL command
> > > > > > > > > > > > (DBD ERROR: OCIStmtExecute/Describe) at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 77.
> > > > > > > > > > > > prepareAndExecute FAILED:
> > > > > > > > > > > > GUS::ObjRelP::DbiDbHandle=HASH(0x81d2150)->errstr
> > > > > > > > > > > > Can't call method "execute" without a package or object reference at
> > > > > > > > > > > > /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 78.
> > > > > > > > > > > >
> > > > > > > > > > > > Some kind of referencing error?  Thanks,
> > > > > > > > > > > >
> > > > > > > > > > > > Michael Luchtan
> > > > > > > > > > > > http://www.cs.uga.edu/~luchtan
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > -------------------------------------------------------
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> > > > > > > > > > > > The only event dedicated to issues related to Linux enterprise solutions
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> > > > > > > > > > > >
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> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > -------------------------------------------------------
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> > > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > > www.enterpriselinuxforum.com
> > > > >
> > > > > _______________________________________________
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> > > > >
> > > >
> > > >
> > > >
> > > > -------------------------------------------------------
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> > > >
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