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Re: [Gusdev-gusdev] Load GOOntology error--
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From: MICHAEL L. <lu...@cs...> - 2003-05-16 18:18:58
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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
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > -------------------------------------------------------
> > > > > > > > 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
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> >
>
>
>
> -------------------------------------------------------
> 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...
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>
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