gusdev-gusdev

[Gusdev-gusdev] LoadPfam plugin error:

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

Hello all
While attempting to use the LoadPfam plugin I have gotten the following
error messages:

[luchtan@mango luchtan]$ ga GUS::Common::Plugin::LoadPfam --release=8.0
--flat_file=/scratch/luchtan/Pfam-A.full --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::Common::Plugin::LoadPfam'
       AND cvs_revision    = '1.8b'


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 (102)


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, 102, 2, 229, 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 (102)

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, 229, 1, 1, 3, 1, 1, 229, 2483, 474, 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, 229, 1, 3, 1, 1, 229, 2484, 480, 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, 229, 1, 3, 1, 1, 229, 2485, 479, 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, 229, 1, /scratch/luchtan/Pfam-A.full, 3,
1, 1, 229, 2486, 477, 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, 229, 1, 3, 1, 1, 229, 2487, 473, 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, 229, 1, /home/luchtan/.gus.properties, 3,
1, 1, 229, 2488, 476, 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, 229, 1, 3, 1, 1, 229, 2489, 482, 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, 229, 1, 3, 1, 1, 229, 2490, 481, 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, 229, 1, 8.0, 3, 1, 1, 229, 2491, 475, 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, 229, 1, 3, 1, 1, 229, 2492, 478, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
ImportPfam: COMMIT OFF
ImportPfam: reading Pfam release 8.0 from /scratch/luchtan/Pfam-A.full
In readExternalDbReleases()
0: PF00244


sqlExec:
    INSERT INTO DoTS.PfamEntry (  row_user_id, alignment_method,
user_write, group_write, accession, row_project_id, group_read,
row_group_id, other_read, release, modification_date, user_read,
number_of_seqs, pfam_entry_id, row_alg_invocation_id, author, definition,
identifier, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?, ?,
?, ? )
  bindValues (6, Clustalw, 1, 1, PF00244, 2, 1, 3, 1, 8.0, 1, 203, 9, 229,
Finn RD, 14-3-3 protein, 14-3-3, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)


sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (229, 229)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Unable to find ID for ExternalDatabase medline at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm line 414, <PFAM>
line 493.



***********************************************
My first thought was to add an entry to the sres.externaldatabase table
like so:
insert into Sres.Externaldatabase
values(95,'medline','medline',SYSDATE,1,1,1,1,1,0,6,3,2,1);
But even after doing so I get the same error.

Does anyone have any ideas?



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

Re: [Gusdev-gusdev] LoadPfam plugin error:

[Jonathan C. <cra...@pc...>]

Michael-

MICHAEL LUCHTAN wrote:
> My first thought was to add an entry to the sres.externaldatabase table
> like so:
> insert into Sres.Externaldatabase
> values(95,'medline','medline',SYSDATE,1,1,1,1,1,0,6,3,2,1);
> But even after doing so I get the same error.
> 
> Does anyone have any ideas?

My guess is that you also need to add an entry to the ExternalDatabaseRelease
table, since (as of version 3.0) GUS has split its representation of external
databases into two tables: ExternalDatabase and ExternalDatabaseRelease.  The
plugin has been updated accordingly, however, the error messages (and comments)
still refer to the old schema (which only has the ExternalDatabase table).
Here's the relevant part of the code.  Line 414 is the "die" statement,
obviously:

 ># Return the external_db_id of an ExternalDatabase given its name.
 >#
 >sub getExtDbRelId {
 >    my($extDbRels, $name) = @_;
 >
 >    $name     =~ tr/A-Z/a-z/; # Normalize to lowercase
 >
 >    my $db    = $extDbRels->{$name};
 >    my $relId = $db->{'external_database_release_id'} if defined($db);
 >
 >    die "Unable to find ID for ExternalDatabase $name" if (not defined($relId));
 >    return $relId;
 >}

I've updated the plugin in CVS to make the comment and error message a
little more accurate.

Looking quickly at the rest of the code, it appears that the "getExtDbRelId"
will always return the most recent ExternalDatabaseRelease (or, rather, its
primary key value) for a given ExternalDatabase.name, based on
ExternalDatabaseRelease.release_date.  This is ever-so-slightly dangerous,
because the release_date is nullable, but should not be an issue so long as
you specify one that's non-null.

Jonathan

Re: [Gusdev-gusdev] LoadPfam plugin error:

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

Hey Jonathan:
I tried adding an entry into esternaldatabaserelease like so:
insert into Sres.Externaldatabaserelease
values(105,95,SYSDATE,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,SYSDATE,1,1,1,1,1,0,6,3,2,1);
which was inserted succesfully.  (I'm not sure what version of the medline
database I'm supposed to use, so I just put 1.  Actually, I don't even see
why the pfam plugin would require this to be there since medline is a
publications database)  Anyway, here is the error I get when executing the
the following:

[luchtan@mango luchtan]$ ga GUS::Common::Plugin::LoadPfam --release=8.0
--flat_file=/scratch/luchtan/Pfam-A.full --verbose
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/.gus.properties
.
.
.

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, 231, 1, 3, 1, 1, 231, 2512, 493, 0)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
ImportPfam: COMMIT OFF
ImportPfam: reading Pfam release 8.0 from /scratch/luchtan/Pfam-A.full
In readExternalDbReleases()


sqlExec:
    UPDATE  Core.AlgorithmInvocation
    SET
	end_time = SYSDATE,
	row_alg_invocation_id = ?,
	modification_date = SYSDATE
    WHERE   algorithm_invocation_id = ?
  bindValues (231, 231)
 DbiHandle:sqlExec:insert succeeded 1 row(s)
Can't use an undefined value as a HASH reference at
/home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm line 285.


Any ideas what the deal here is?

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


On Thu, 29 May 2003, Jonathan Crabtree wrote:

>
> Michael-
>
> MICHAEL LUCHTAN wrote:
> > My first thought was to add an entry to the sres.externaldatabase table
> > like so:
> > insert into Sres.Externaldatabase
> > values(95,'medline','medline',SYSDATE,1,1,1,1,1,0,6,3,2,1);
> > But even after doing so I get the same error.
> >
> > Does anyone have any ideas?
>
> My guess is that you also need to add an entry to the ExternalDatabaseRelease
> table, since (as of version 3.0) GUS has split its representation of external
> databases into two tables: ExternalDatabase and ExternalDatabaseRelease.  The
> plugin has been updated accordingly, however, the error messages (and comments)
> still refer to the old schema (which only has the ExternalDatabase table).
> Here's the relevant part of the code.  Line 414 is the "die" statement,
> obviously:
>
>  ># Return the external_db_id of an ExternalDatabase given its name.
>  >#
>  >sub getExtDbRelId {
>  >    my($extDbRels, $name) = @_;
>  >
>  >    $name     =~ tr/A-Z/a-z/; # Normalize to lowercase
>  >
>  >    my $db    = $extDbRels->{$name};
>  >    my $relId = $db->{'external_database_release_id'} if defined($db);
>  >
>  >    die "Unable to find ID for ExternalDatabase $name" if (not defined($relId));
>  >    return $relId;
>  >}
>
> I've updated the plugin in CVS to make the comment and error message a
> little more accurate.
>
> Looking quickly at the rest of the code, it appears that the "getExtDbRelId"
> will always return the most recent ExternalDatabaseRelease (or, rather, its
> primary key value) for a given ExternalDatabase.name, based on
> ExternalDatabaseRelease.release_date.  This is ever-so-slightly dangerous,
> because the release_date is nullable, but should not be an issue so long as
> you specify one that's non-null.
>
> Jonathan
>
>
>
>