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Re: [Gusdev-gusdev] Load GOOntology error--
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From: MICHAEL L. <lu...@cs...> - 2003-05-16 16:04:13
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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.
prepareAndExecute: SELECT *
FROM Core.AlgorithmImplementation
WHERE executable = 'GUS::GOPredict::Plugin::LoadGoOntology'
AND cvs_revision = '1.11'
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 (90)
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, 90, 2, 174, 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 (90)
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, 174, 1, 1, 3, 1, 1, 174, 1759, 307, 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, 174, 1, 3, 1, 1, 174, 1760, 315, 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, 174, 1, 3, 1, 1, 174, 1761, 309, 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, 174, 1, 3, 1, 1, 174, 1762, 320, 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, 174, 1, 3, 1, 1, 174, 1763, 317, 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, 174, 1, 1, 3, 1, 1, 174, 1764, 310, 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, 174, 1, /home/gusdev/gus3.0-checkouts/GO,
3, 1, 1, 174, 1765, 318, 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, 174, 1, 3, 1, 1, 174, 1766, 321, 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, 174, 1, 3, 1, 1, 174, 1767, 313, 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, 174, 1, 3, 1, 1, 174, 1768, 324, 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, 174, 1, 3, 1, 1, 174, 1769, 316, 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, 174, 1, /home/luchtan/gus.properties, 3,
1, 1, 174, 1770, 308, 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, 174, 1, /home/luchtan/GOLOG, 3, 1, 1, 174,
1771, 323, 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, 174, 1, 3, 1, 1, 174, 1772, 312, 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, 174, 1, 3, 1, 1, 174, 1773, 319, 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, 174, 1, 3, 1, 1, 174, 1774, 322, 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, 174, 1, 3, 1, 1, 174, 1775, 314, 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, 174, 1, 3, 1, 1, 174, 1776, 311, 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
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
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, 93, 174, 1, 2.690, 0, 3)
DbiHandle:sqlExec:insert succeeded 1 row(s)
Thu May 15 23:59:49 2003 successfully submitted new entry into
SRes.ExternalDatabaseReleaseId with primary key of 93
Thu May 15 23:59:49 2003 making root node for function
sqlExec:
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, ?, ?,
?, ?, ?, ? )
bindValues (6, GO:0003673, 1, 1, 1, 2, Gene_Ontology, 93, 1, 0, 3, 3, 1,
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
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > -------------------------------------------------------
> > > > > > Enterprise Linux Forum Conference & Expo, June 4-6, 2003, Santa Clara
> > > > > > The only event dedicated to issues related to Linux enterprise solutions
> > > > > > www.enterpriselinuxforum.com
> > > > > >
> > > > > > _______________________________________________
> > > > > > Gusdev-gusdev mailing list
> > > > > > Gus...@li...
> > > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>
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